explain xkcd - User contributions [en]

1605: DNA

2015-11-19T00:50:53Z

Dsollen: /* Explanation */

{{comic
| number = 1605
| date = November 18, 2015
| title = DNA
| image = dna.png
| titletext = Researchers just found the gene responsible for mistakenly thinking we've found the gene for specific things. It's the region between the start and the end of every chromosome, plus a few segments in our mitochondria.
}}

==Explanation==
Because we have pretty much {{w|Human Genome Project|mapped the entire human Genome}}, it's tempting to think we now know what makes our bodies tick and can start changing things. But just knowing what the individual pieces are, doesn't mean we know how they interact and behave in a complex system like our bodies.

In the comic, [[White Hat]] thinks that mapping the human genome is the same as knowing the {{w|source code}} for a {{w|computer program}}. By studying the source code for a program, a person can often understand why it does what it does, and make effective and fundamental changes to the program's operation. [[Megan]] tries to point out to him, that while in theory that could be the case with the human body, the reality is the human body is of such a magnitude more complicated than the kinds of programs we have running that the comparison is not valid. White Hat is not ready to listen to her even though she states that {{w|DNA}} has been developed in the most aggressive optimization process in the universe, running for billions of years. White Hat's thought process is similar to the physicist in [[793: Physicists]] who assumes that any other field is simple because it's similar to something he's seen before.

Finally Megan {{w|Hacker koan|enlightens}} White Hat by making him look at {{w|Google}}'s source code. On the surface, it looks like a very plain white page with a search box in the middle plus a few text links and icons, and indeed back in the 1990s Google's {{w|HTML}} was quite simple. But in less than 20 years, Google developers have vastly expanded it with over 300 kilobytes of {{w|Minification (programming)|minified}} Javascript and CSS. This analogy causes White Hat to consider how much more complexity could evolve over billions of years through the relentless forces of nature.

What makes this even worse for DNA is that although it can be thought of 'source code' it isn't for a comprehensive language, and that this code was generated through various natural mechanisms such as {{w|natural selection}}, feedback loops like {{w|homeostasis}}, etc., even including possible processes that are not currently known to science. This means that not all parts make sense and that there may by all kinds of side effects and things that have several purposes. Looking at some obfuscated source code may make it clearer how misleading even simple looking code can be and how unreadable correct and well working code can be.

The title text reference to finding the gene that is responsible "for mistakenly thinking we've found the gene for specific things" is a reference to the tendency of news organizations to run headlines making similar claims, often by oversimplifying or misrepresenting the actual study. These claims are based off the common belief that since DNA is a 'source code' for our body it should be possible to pin point the effect of individual genes in much the same way that we could describe the effect each line of code has on a program; leading to people expecting one gene to be associated with each observable human trait. In reality even small traits are the results of hundreds of genes, sometime spread across multiple chromosomes, interacting together through complex mechanisms; making it rare that a single gene, or gene sequence, can be definitively stated to be the sole, or primary, cause of a given trait.

The jokes of the title text is that is that the responsible gene is located in ''the region between the start and the end of every chromosome'' which is the whole {{w|chromosome}}, effectively claiming that it is the whole of our DNA, not any one piece, that must be considered responsible for the referenced trait, since the interconnected nature of DNA means that every gene is partially responsible in generating any complex traits. [[Randall]] even includes the {{w|mitochondria}} stating that the gene could also be in some segments of the mitochondrion. Mitochondrion is a part of the cell that are outside the cell-nucleus. The chromosome is located in the nucleus, but the Mitochondria has its own independent genome, so some part of the human DNA is not located in the chromosomes. This makes it really complex, and makes it even less distinct where this gene should be and it implies that all of our genes make us think we've found the gene for specific things.

Technically a gene is "a locus (or region) of DNA that encodes a functional RNA or protein product", which means that it is a single discrete unit of DNA, with human DNA containing over 20,000 genes. Thus the theoretical gene could not include the entire ''region between the start and the end of every chromosome'' since that region contains thousands of genes, any more then it's possible to say that the ace of clubs is the card everywhere from the top of the full deck of cards to the bottom of it.

Of course if such a gene actually did exist, then we would never be able to correctly identify where it was since we would make a mistake every time we thought we found a gene for something specific. So the whole title text is either a {{w|contradiction}} (they could never find this gene if it was there) and/or it is a {{w|Tautology (logic)|tautology}} since if the gene did exist, then of course it has to be part of our entire DNA. (If it is a tautology it is the second title text using this in just two weeks, the last being [[1602: Linguistics Club]].)

==Transcript==
:[White Hat, holding a laptop, is talking to Megan who looks at her smart phone.]
:White Hat: Biology is largely solved. DNA is the source code for our bodies. Now that gene sequencing is easy, we just have to read it.
:Megan: It's not just "source code". There's a ton of feedback and external processing.

:[White Hat, opening his laptop, walks toward a desk and chair past Megan who holds her arms out.]
:Megan: But even if it were, DNA is the result of the most aggressive optimization process in the universe, running in parallel at every level, in every living thing, for four billion years.
:White Hat: It's still just code.

:[White Hat sits down at the desk with his opens laptop, while Megan looks over his shoulder.]
:Megan: OK, try opening google.com and clicking "View Source."
:White Hat: OK,I-...Oh my god.
:Megan: That's just a few years of optimization by Google devs. DNA is thousands of times longer and way, way worse.
:White Hat: Wow, biology is ''impossible''.

{{comic discussion}}

[[Category:Comics featuring White Hat]]
[[Category:Comics featuring Megan]]
[[Category:Programming]]
[[Category:Computers]]
[[Category:Biology]]
[[Category:Science]]

Talk:1605: DNA

2015-11-19T00:49:32Z

Dsollen:

The source for Google.com can be found at `<nowiki>view-source:https://www.google.com/</nowiki>` for Firefox and Chrome. Also [http://pastebin.com/raw.php?i=u8SMf7G6 here]. —[[User:Artyer|Artyer]] <sup><big>([[User Talk:Artyer|talk]]<big>'''|'''</big><sub>[[Special:Contributions/Artyer|ctb]]</sub>)</big></sup> 16:06, 18 November 2015 (UTC)
:Should there be a link to the code in the explain. I do not understand these links or the source code, and would not like to place these links in the explanation. --[[User:Kynde|Kynde]] ([[User talk:Kynde|talk]]) 18:43, 18 November 2015 (UTC)

I really like this comic. IMHO, just another good example of intelligent design. Google's dev had to design, plan and carefully code. If that is seemingly simple compared to DNA and biology then how much more intelligence and thought was needed for the coding of all living things?--[[User:R0hrshach|R0hrshach]] ([[User talk:R0hrshach|talk]]) 17:18, 18 November 2015 (UTC)
:With all the stupid things going on in our bodies (rendered useless by natural selection but staying put anyway like the {{w|Appendix (anatomy)|Appendix}} or our {{w|tailbone}}) then it is to me just a clear example that there has been no intelligence behind our genome, but just trial and error, and then 4 billion years to get it right enough that it works but not smart. And don't get me started on how our air and food/drink has to go in the same way with the risk of being (nearly) killed by a pretzel...([http://www.dailymail.co.uk/news/article-94567/I-feel-great-President-Bush-declares-pretzel-incident.html even if you are the president of the US] ;-) That is just plain stupid design. But few enough dies from this, that it was necessary for nature to change it once it was working. Humans and the genes survived long enough to reproduce. --[[User:Kynde|Kynde]] ([[User talk:Kynde|talk]]) 18:43, 18 November 2015 (UTC)

Apologies, when I saved my comments it blitzed someone else's that must have been being written at the same time :'-( [[User:RIIW - Ponder it|RIIW - Ponder it]] ([[User talk:RIIW - Ponder it|talk]]) 19:13, 18 November 2015 (UTC)
:Yeah it was my two comments above? I have now moved the one right her above back in place from the bottom where Davidy22 had placed it when he tried to fix it. No harms done but as he says: ''Read error messages, I know mediawiki gives them to you''. You can always see in the history what you have changed. --[[User:Kynde|Kynde]] ([[User talk:Kynde|talk]]) 21:08, 18 November 2015 (UTC)
::I, for my part read the edit conflict (with Kynde, 18:43) like a good little boy, re-edited in light of that, resubmitted and... forgot to answer the security question. For completeness I wrote the following. If it's still helpful...
Had the same thought. Although I just use "View | Source" from the menu or right-click and "View Page Source", or whatever that browser tends to want to give me. And, having had that same thought: For reference, in case anybody wants it, the source of the google.co.uk main page (assumed not far off google.com in its nature) is 51 lines. But that's 51 ''long'' lines of mostly javascript, with much of the unnecessary whitespace (including line-feeds) taken out of it, overwhelmingly single-character variable names, over 150 'if' statements (including 'else if' ones, in continuation to a prior one) and perhaps 56 'for' loops, at first glance. Whether 'optimised' or obfuscated, it certainly could be a challenge to fully understand.
:: HTH, HAND [[Special:Contributions/141.101.106.161|141.101.106.161]] 21:43, 18 November 2015 (UTC)

IMHO DNA with its redundant sections for things not currently used and the bodges in biological design are a good example of unintelligent design. For example the blood supply to the retina is between the iris and the retina, so it is in the way. An intelligent designer would do an eye mark II. But this has nothing to do with the comic. [[User:RIIW - Ponder it|RIIW - Ponder it]] ([[User talk:RIIW - Ponder it|talk]]) 19:07, 18 November 2015 (UTC)

White Hat is showing the hubris often seen by people who think their (often limited) knowledge in one field can be used as an anology for something very different. Megan only manages to showchim his error by showing that a "simple" web page, which has only been evolving for a few years is more complex than he thinks, and the role of any one line/command in the page is probably far from clear without deep analysis [[User:RIIW - Ponder it|RIIW - Ponder it]] ([[User talk:RIIW - Ponder it|talk]]) 19:07, 18 November 2015 (UTC)

The evolution of life is composed exclusively of copy-paste programming on top of legacy code, global variables, and hacks on hacks on hacks at every level, from telomeres and DNA looping, to the structure of the human hip (childbirth), to our breathing tract, optic nerve, and brain structure and cognition. --[[Special:Contributions/199.27.130.234|199.27.130.234]] 21:47, 18 November 2015 (UTC)
: That's what you get when you hack the universe together with perl.

1605: DNA

2015-11-19T00:44:04Z

Dsollen: /* Explanation */

{{comic
| number = 1605
| date = November 18, 2015
| title = DNA
| image = dna.png
| titletext = Researchers just found the gene responsible for mistakenly thinking we've found the gene for specific things. It's the region between the start and the end of every chromosome, plus a few segments in our mitochondria.
}}

==Explanation==
Because we have pretty much {{w|Human Genome Project|mapped the entire human Genome}}, it's tempting to think we now know what makes our bodies tick and can start changing things. But just knowing what the individual pieces are, doesn't mean we know how they interact and behave in a complex system like our bodies.

In the comic, [[White Hat]] thinks that mapping the human genome is the same as knowing the {{w|source code}} for a {{w|computer program}}. By studying the source code for a program, a person can often understand why it does what it does, and make effective and fundamental changes to the program's operation. [[Megan]] tries to point out to him, that while in theory that could be the case with the human body, the reality is the human body is of such a magnitude more complicated than the kinds of programs we have running that the comparison is not valid. White Hat is not ready to listen to her even though she states that {{w|DNA}} has been developed in the most aggressive optimization process in the universe, running for billions of years. White Hat's thought process is similar to the physicist in [[793: Physicists]] who assumes that any other field is simple because it's similar to something he's seen before.

Finally Megan {{w|Hacker koan|enlightens}} White Hat by making him look at {{w|Google}}'s source code. On the surface, it looks like a very plain white page with a search box in the middle plus a few text links and icons, and indeed back in the 1990s Google's {{w|HTML}} was quite simple. But in less than 20 years, Google developers have vastly expanded it with over 300 kilobytes of {{w|Minification (programming)|minified}} Javascript and CSS. This analogy causes White Hat to consider how much more complexity could evolve over billions of years through the relentless forces of nature.

What makes this even worse for DNA is that although it can be thought of 'source code' it isn't for a comprehensive language, and that this code was generated through various natural mechanisms such as {{w|natural selection}}, feedback loops like {{w|homeostasis}}, etc., even including possible processes that are not currently known to science. This means that not all parts make sense and that there may by all kinds of side effects and things that have several purposes. Looking at some obfuscated source code may make it clearer how misleading even simple looking code can be and how unreadable correct and well working code can be.

The title text reference to finding the gene that is responsible "for mistakenly thinking we've found the gene for specific things" is a reference to the tendency of news organizations to run headlines making similar claims, often by oversimplifying or misrepresenting the actual study. These claims are based off the common belief that since DNA is a 'source code' for our body it should be possible to pin point the effect of individual genes in much the same way that we could describe the effect each line of code has on a program; leading to people expecting one gene to be associated with each observable human trait. In reality even small traits are the results of hundreds of genes, sometime spread across multiple chromosomes, interacting together through complex mechanisms; making it rare that a single gene, or gene sequence, can be definitively stated to be the sole, or primary, cause of a given trait.

The jokes of the title text is that is that the responsible gene is located in ''the region between the start and the end of every chromosome'' which is the whole {{w|chromosome}}, effectively claiming that it is the whole of our DNA, not any one piece, that must be considered responsible for the referenced trait, since the interconnected nature of DNA means that every gene is partially responsible in generating complex traits such as our desire to try to associate genes to specific aspects. [[Randall]] even includes the {{w|mitochondria}} stating that the gene could also be in some segments of the mitochondrion. Mitochondrion is a part of the cell that are outside the cell-nucleus. The chromosome is located in the nucleus, but the Mitochondria has its own independent genome, so some part of the human DNA is not located in the chromosomes. This makes it really complex, and makes it even less distinct where this gene should be and it implies that all of our genes make us think we've found the gene for specific things.

Technically a gene is "a locus (or region) of DNA that encodes a functional RNA or protein product", which means that it is a single discrete unit of DNA, with human DNA containing over 20,000 genes. Thus the theoretical gene could not include the entire ''region between the start and the end of every chromosome'' since that region contains thousands of genes, any more then it's possible to say that the ace of clubs is the card everywhere from the top of the full deck of cards to the bottom of it.

Of course if such a gene actually did exist, then we would never be able to correctly identify where it was since we would make a mistake every time we thought we found a gene for something specific. So the whole title text is either a {{w|contradiction}} (they could never find this gene if it was there) and/or it is a {{w|Tautology (logic)|tautology}} since if the gene did exist, then of course it has to be part of our entire DNA. (If it is a tautology it is the second title text using this in just two weeks, the last being [[1602: Linguistics Club]].)

==Transcript==
:[White Hat, holding a laptop, is talking to Megan who looks at her smart phone.]
:White Hat: Biology is largely solved. DNA is the source code for our bodies. Now that gene sequencing is easy, we just have to read it.
:Megan: It's not just "source code". There's a ton of feedback and external processing.

:[White Hat, opening his laptop, walks toward a desk and chair past Megan who holds her arms out.]
:Megan: But even if it were, DNA is the result of the most aggressive optimization process in the universe, running in parallel at every level, in every living thing, for four billion years.
:White Hat: It's still just code.

:[White Hat sits down at the desk with his opens laptop, while Megan looks over his shoulder.]
:Megan: OK, try opening google.com and clicking "View Source."
:White Hat: OK,I-...Oh my god.
:Megan: That's just a few years of optimization by Google devs. DNA is thousands of times longer and way, way worse.
:White Hat: Wow, biology is ''impossible''.

{{comic discussion}}

[[Category:Comics featuring White Hat]]
[[Category:Comics featuring Megan]]
[[Category:Programming]]
[[Category:Computers]]
[[Category:Biology]]
[[Category:Science]]