Main Tropes Index

Troperville

Editing Help

Tools

Toys

Narrative

• Universal
• Applied Phlebotinum
• Characterization
• Characters
• Characters As Device
• Dialogue
• Motifs
• Narrative Devices
• Paratext
• Plots
• Settings
• Spectacle

Genre

• Action Adventure
• Comedy
• Commercials
• Crime And Punishment
• Drama
• Horror
• Love
• News
• Professional Wrestling
• Speculative Fiction
• Sports Story
• War

Media

• Animation (Western)
• Anime
• Comic Book
• Fan Fics
• Film
• Game
• Literature
• Music And Sound Effects
• New Media
• Print Media
• Radio
• Sequential Art
• Tabletop Games
• Television
• Theater
• Videogame
• Webcomics

Topical Tropes

• Betrayal
• Censorship
• Combat
• Death
• Family
• Fate And Prophecy
• Food
• Holiday
• Memory
• Money
• Morality
• Politics
• Religion
• School

Other Categories

• British Telly
• The Contributors
• Creator Speak
• Creators
• Derivative Works
• Did Not Do The Research
• Language
• Laws And Formulas
• Show Business
• Split Personality
• Stock Room
• Trope
• Truth And Lies
• Truth In Television
• Weirdness Isolation

Haven: Took out Nano Jackal as an example of Badass Normal, as her nanos gave her Improbable Aiming Skills—they let her richochet her bullet off the one guy's gun into the other's head, you know.

---

Uknown Troper: I took out the following parts:

• Did Not Do The Research: For all the author's attempts to mock the poor genetics associated with the series, he makes almost as many mistakes as the games themselves, in particular his thoroughly misguided 'recessive does not mean inferior' rant. In context [speaking about the recessive alleles of an organism with a phenotype determined superior for a given application] it actually does mean exactly that, as recessive in the context of a single organism's genome means 'unexpressed.'
  • Since this seems to be confusing people, further explanation: Liquid Snake is talking about the DNA of a single creature, Big Boss. In the context of one creature's DNA, 'recessive' means a trait which is not expressed, while 'dominant' means a trait which is expressed over a recessive one. In this context, 'double recessive' or 'double dominant' is meaningless; when both alleles are the same, there is no dominant-recessive relationship since neither prevents the other being expressed. Of course it's a little more complex than that, but that doesn't factor into explaining this.
  • Les Enfants Terribles has determined Big Boss is a genetically superior soldier. This means the traits he expresses make him that way. Since they're spoken of in terms of being dominant and recessive, it follows that the dominant [expressed] traits are what make him that way, while the recessive [unexpressed] traits do not, and are, by the standard the project has set, inferior. This is not the same as saying all recessive traits are inferior in every way to all dominant traits; Liquid only ever speaks in terms of Big Boss' DNA and the 'soldier genes.'
  • Focusing on this means the comic misses out on the real Wall Banger, that this was done 'to create a phenotype in which all the dominant genes [alleles] were expressed.' By definition, this was already happening in Big Boss' own phenotype, since 'expressed in the phenotype' is what 'dominant' means in this context. In other words, the whole recessive / dominant clone stage was pointless; straight clones of Big Boss would have expressed all his dominant traits anyway, since he did himself. The idea of Solidus, a 'perfect blend of dominant and recessive' is even more ludicrous, since if Big Boss' superior soldier traits were recessive as per the definition above, he wouldn't have had them himself!
• You Fail Biology Forever: Mostly the author.

Ok, where to start, where to start? In this comic, the author, who seems to have some knowledge of genetics, tries to make light of Hideo Kojima's rather tenous grip on genetics (or at least that possessed by the characters he writes), especially the whole 'recessive gene, dominant gene' debacle around Liquid and Solid. First of all, although it's poor form, let's open this with a little quotation:

"Remember, genes are not blueprints. This means you can't, for example, insert "the genes for an elephant's trunk" into a giraffe and get a giraffe with a trunk. There are no genes for trunks. What you can do with genes is chemistry, since DNA codes for chemicals."

—Academician Prokhor Zakharov, Sid Meier's Alpha Centauri

Within genetics, the term "dominant" is mostly a contextual term — the term "recessive" means a gene's product will be downregulated, and usually not expressed, as long as a gene that is "dominant" to it is found on the other locus of the gene. This much is obvious. What this doesn't mean, however, is that all genes follow a simple recessive/dominant dualism. In fact, we have very, very, very little information on how the virtually thousands of variations found in the approximately, oh, 30-40,000 genes (never mind things like alternate splicing and whatnot) in the human genome interact with each other — in many cases, the end result probably is a combination of the two traits that are expressed side-by-side, because not everything is as easy to quantify as hair or eye colour, or the colour of pea blossoms used by Mendel when he laid the foundation for genetics. There are terms such as co-dominance, incomplete and semi-dominance, and equally clear-cut examples for those (let's say, Immunoglobulin genes, or blood type; co-dominant both of them except for O blood type) that indicates that things aren't that easy.

As my quotation was intended to reveal, genes code for proteins. In Big Boss' case, his 'genetic superiority' comes from the fact that a combination of genes found on his various loci gives him a genetic disposition towards good muscle build, agility, high IQ, etc., and even if we are to accept that this 1970s project somehow managed to map his entire genome and find all his genes and their relevance for his soldier abilities (something that is likely impossible today; we're basically taking the first baby steps that allows us to find certain well-known genetic diseases, nevermind the combination of genes that produce an interlocking set of proteins resulting in good muscle tissue), the odds that all said genes are divided into a simple "dominant"/"recessive" dichotomy is, to put it nicely, ludicrous, as is the assumption that just because a gene's expression is downregulated by its other loci it is automatically 'inferior': Genetic diseases inhabit both recessive and dominant alleles, but we don't learn about most of the former because people who somehow end up with them (through spontaneous mutation, or by getting a diseased dominant gene without a requisite mutation of an interacting gene that undos the effects of the disease) tend to die out — dwarfism, for instance, is a 'dominant' genetic trait (and incidentally also an incompletely dominant one — the recessive 'normal' gene allows growth to a functional state, and people with double dwarf mutations are spontaneously aborted).

To summarize, the question of 'context' here is silly, and not at all a question of whether the author Did Not Do The Research — sure, the comic not a Master's Thesis in "The Rape of the Laws of Genetics Done by Hideo Kojima", but it clearly isn't supposed to be, it's supposed to be funny. Mantis, however coloured his language is, gets the basic concept across — the idea of "dominant" automatically meaning "superior" and "recessive" meaning "inferior" is bull, as is your already pointed out Wall Banger about the concept of 'clones' that only inherit half of your genome (both of whom would likely have died from genetic diseases or complications brought on from identical alleles — as for Solidus, he's either equally freakish as the other two or just the only semi-sanely-made clone of the trio). Frankly, I just buy the whole thing as something Big Boss made up to egg on Liquid, who clearly doesn't know better.

And besides, if Liquid has all of Big Boss' "dominant" genes, why the heck does he have the recessive hair- and eye colour anyway?

---

Within genetics, the term "dominant" is mostly a contextual term — the term "recessive" means a gene's product will be downregulated, and usually not expressed, as long as a gene that is "dominant" to it is found on the other locus of the gene. This much is obvious. What this doesn't mean, however, is that all genes follow a simple recessive/dominant dualism.

• The phrase 'so what?' comes to mind. In an individual where a recessive / dominant dualism is established, they do indeed do that, and given the talk about dominants and recessives, that must be what is going on with Big Boss' genes. You're making the same mistake as the author in talking about alleles in the context of a population rather than what's present in one person. Also, you mean 'allele,' not 'gene.'

There are terms such as co-dominance, incomplete and semi-dominance, and equally clear-cut examples for those (let's say, Immunoglobulin genes, or blood type; co-dominant both of them except for O blood type) that indicates that things aren't that easy.

• Which have no bearing on anything here. The 'soldier gene' alleles are clearly all simple dominant-recessive pairings, that is made abundantly clear.

the odds that all said genes are divided into a simple "dominant"/"recessive" dichotomy is, to put it nicely, ludicrous

• The odds of something that has happened happening are 1. We're not dealing with a possiblity in-universe, it is a fact that that is how the 'soldier genes' are divided, no matter how unlikely it is. It is clear even in the universe that Big Boss is a fantastically rare specimen, hence the efforts to copy him in the first place.

as is the assumption that just because a gene's expression is downregulated by its other loci it is automatically 'inferior'

• Which I actually addressed in the section you removed. The assumption is not that a recessive allele is necessarily inferior regardless of the situation, it is that when it has been established that one person posesses a superior phenotype for a specific goal, his unexpressed traits will not help you recreate it. This means they are inferior because they do not make the thing you want to make.

Mantis, however coloured his language is, gets the basic concept across — the idea of "dominant" automatically meaning "superior" and "recessive" meaning "inferior" is bull

• Neither is it present in Metal Gear Solid, which is the mistake the author makes. In fact, the debunking popular with fans is bull, as that isn't what Liquid was saying. Again: he is saying Big Boss' expressed traits make him a superior soldier. Therefore, his unexpressed traits do not have anything to do with that, and a genome built to express them will be inferior by the standards the project has set out. 'Superior' by the definition used by Les Enfants Terribles simply means 'like Big Boss.'

• Let's say as a casual example that I've built a machine that will kill anyone who has blonde hair. For the goal of surviving walking through the machine, people who have the recessive blonde-haired trait are going to be worse than people who have the dominant dark-haired trait. This does not mean that people with blonde hair are worthless at everything in the entire universe, but if we're just discussing this project, it would not be wrong to say they are 'inferior.' Change 'walking through blonde people killing machine' to 'being like Big Boss' and you have the situation here; the recessive traits are called 'inferior' because they don't produce a desired result. From the project's perspective, they're just junk, no matter what they actually do.

And besides, if Liquid has all of Big Boss' "dominant" genes, why the heck does he have the recessive hair- and eye colour anyway?

• He doesn't. Depending on when in the series you are, Snake is a natural blonde [Shinkawa was talking about Big Boss being blonde as late as dev work for MGS 2, and Snake is clearly fair haired in the intro to MGS when he's naked, even when he isn't under a harsh light, that scene was even altered to make him dark haired in Twin Snakes], or Liquid is dark haired [the later reasoning is that Liquid's hair was 'bleached in the sun' during his time in the middle east]. Either way, they both have the same colour hair. MGS 1 characters don't have eyes, so I'm not sure what you're talking about there.

Uknown Troper: ...Ok, let me try to approach this from a different angle:

First of all, the "the soldier genes follow a clear dominant/recessive dichotomy" part isn't made abundantly clear. Nowhere in either the comics, or the game series, or anywhere, are the dualism status of the 'soldier genes' made clear to me — in fact, if anything, the comic openly rebels against such a simplistic notion. In other words, we don't know this has happened. All we have are the words of Big Boss, a man who is by his own admission a liar using a psychological tactic to egg on Liquid with bullshit genetics. If you want to make that point, source it from a sufficently reputable source. Unless proven otherwise, Big Boss' genes probably work like those of most real people and his expressed traits are not, necessarily, a question of only 'dominant' alleles being expressed, but rather a mixture of all alleles in all his genetic loci. In fact, I'd go so far as to state that your context of 'all soldier genes are dominant/recessive' and thus 'desired by project = dominant trait' is entirely a question of your personal interpretation and in no way based either on comic or game source material — it's fairly clear that Liquid is, to put it nicely, ignorant of the nuances of genetics.

Besides, gene expression is in many ways regulated by nurturing, with genes being expressed at different levels due to factors such as training, diet, etc, so calling a character 'inferior' based purely on genetic material without taking into account how the genes get expressed during growth is silly, and I'd presume anyone intelligent enough to run a human cloning operation would also be intelligent enough to know not to assign something 'success' or 'failure' based entirely on a gene readout without taking into account how the traits are actually expressed during growth of the unit, as this is a violation of the Scientific Method on its most basic level. Of course, for all I know, the project has a giant dumpster filled with a few hundred dead earlier-attempt clones at various stages of growth to give them sufficient empirical indications on which to base such assumption.

But, you know, all of this is moot, because the author of the comics is working from his knowledge in real-world genetics and biology as a platform for mocking the Metal Gear Solid view. Whether or not it works like that in Metal Gear Solid ultimately doesn't matter, because the standards it is judged it by in the comic, and what the comedy is based on, is how things work in Real Life and how grotesquely bizarre the story's understanding of genetics come across to characters versed in genetics based in real life. The Did Not Do The Research and You Fail Biology Forever tropes explicitly adhere to the concept of writers not understanding the Real Life sciences they base their technobabble on, which is not at all the case here — at best, this comic lampshades the idiocy of trying to play it as simply as "all genes follow dominant/recessive dualism" and the following argument that "within context, dominant equals superior".

In other words, you can argue semantics as much as you want, but this does not fall under the trope in question: Mantis' rant is entirely correct within the confines of Real World mendelian genetics. If real world genetics worked like how you're trying to present Metal Gear Solid's did, that would make it a case. Or possibly you could have made the comic a case of not having done the research on how the Metal Gear Solid universe works, but since the comic is an obvious parody it's no point trying to argue it works that way, either.

---

You've failed to really provide any good reasoning for your case here. The rant says that Liquid is saying the alleles in question are superior because they are dominant. He is not saying this; he says that the dominant alleles are superior because they are the expressed traits of a genetically superior soldier. This is absolutely, entirely accurate. The author's rant is basically beating up a strawman based on a line that only exists inside his head. His claim that 'dominant and recessive are just terms they teach middle schoolers' is also dubious, since there are alleles of genes which have simple absolute dominant / absolute recessive relationships and follow basic Mendelian principles. Your decrying the plausibility of such relationships doesn't speak well of your own knowledge of genetics [nevermind constantly using the word 'locus' while mixing up 'allele' and 'gene'] and I must wonder how much of this you're just bullshitting using Wikipedia; certainly, you don't know what "Mendelian genetics" refers to, since you're arguing against it being a simple absolute dominant / absolute recessive situation. Mantis' rant not only doesn't work within Mendelian genetics, it actually totally denies Mendelian inheritance exists at all. I've got a Biology A Level, so you might want to stop waving the author's alleged credentials around while you're at it.

Moreover, it is clear from the discussion in Metal Gear Solid that this is how it works; I believe Liquid says LET identified 40 "soldier genes" that Big Boss had superior versions of in his phenotype. Rather than being for physical traits, the examples he actually gives are related to brain chemistry; he lists "strategic thinking" and "the proverbial killer instinct" as examples of what they govern. It's clear from the dominant clone / recessive clone mechanics of the project that these 40 genes each had a fully dominant and a fully recessive allele in Big Boss' genome. The big mistake made is the assumption that there would be some kind of need to make a double-dominant clone to duplicate Big Boss' phenotype, when by definition it doesn't matter if you're dominant-recessive or double-dominant. The idea that they'd want the dominant traits is not an error, and the novelisation actually screwed up by saying it was [it has Clarke smugly note that the US president is wrong to want the dominant clone, when actually he's correct; never let a medic do genetics, I guess].

Also, I removed MGS from the Lego Genetics examples, because it isn't one; the LET children were altered at conception [though it's never clear when they swapped Solid's dominant 'soldier' alleles to Liquid and vice versa, since according to Liquid that was after they'd aborted six of the eight embryos], and the Genome Soldiers aren't what it's talking about; Lego Genetics would be giving them gorilla DNA to make them strong, hawk DNA to improve their vision and so on [as was popular with villians in 80s and 90s cartoons], not a gene therapy course with serious side-effects and very little obvious benefit to the recipients.

---

Uknown Troper: Well, I'm very sorry to hear that. Then, if it is the quality of the message you're concerned with rather than trying to actually refute any of my claims, allow me to state and source my statements properly to remove uncertainties on that part. In other words, I'm taking the burden of proof for this round and expect you to do the same when you respond. Let's start with getting it straight from the horse's mouth, shall we? Seeing how we're talking about Liquid, let's get his statements straight.

Just as a disclaimer first, however: What I will be using of universe-related material to build my argument are two sources: A) Metal Gear Solid, the game (or in this case the Twin Snakes remake — I doubt the script was changed that much in that regard), and B) The Last Days Of Foxhound, the comic. For the purposes of my argument, I don't consider Metal Gear Solid 2 to have any particular new info on this subject (correct me if I'm wrong), Metal Gear Solid 3 was released after the game, and as for other non-game side material the comic writer may at best not have had access to it, and at worst its canonicity and validity of any such materials may be suspect. I'm also going to concentrate on strips 54-56 in the comic, as these appear to be the main crux of the issue.

With that aside, I managed to find the following three quotes by Liquid by digging through the Metal Gear Solid archives (bolding is mine).

So, what can be made out of the above, with more guess- or interpretation-based statements being built based on the above. Keeping in mind that we are treating the quotes as the only canon at the moment, and taking Liquid's word for all of it (nevermind backstory and whatnot):
— First of all, Liquid uses the very definite term 'dominant vs recessive' in terms of genes, not alleles, and mentions that his own 'recessive genes' are 'inferior' without any stated justification beyond them being 'recessive'.
— The 'soldier genes' were identified as part of the Human Genome Project (1990-2003 in Real Life (source:http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml), Metal Gear Solid doesn't say when its was); I would presume Liquid would have mentioned it earlier if it had been part of the 'Les Enfants Terrible' project.
— In other words, it would follow that the identification of the soldier genes post-dates the creation of Liquid, Solid and Solidus: Liquid and Solid were created in a pre-HGP time-period, with Liquid apparently serving as a guinea pig to give Solid all the 'dominant genes' and leaving him only the 'recessive, inferior genes'.
— Following the identification of the 'soldier genes' they were tested on adult humans during the Gulf War: The results were used to create the Genome Soldiers by an undefined means.
— Metal Gear Solid takes place in 2005, per the game's canon. This makes the time space between starting of the tests that predated the Genome Soldiers and the events of the game 2005-1991=16 years. In other words, either Liquid's army consists exclusively of people below enlistment age (18 in the United States; 17 with parental consent), or the Genome Soldiers were modified post-conception with the so-called 'soldier genes'. Also, unless the genome soldiers are trained using a Tykebomb program (they might, but I highly doubt it) they were modified after joining the army, making the expression of any 'soldier genes' a case of Lego Genetics (not that we ever see any concrete evidence in-game of this having happened, again to my knowledge).
— Liquid's use of 'dominant genes' and his statement of 'To create a phenotype in which all of the dominant genes were expressed, to create you' indicates that he is probably not trained in genetics, or is aware of most of its nuances: Both of the statements are quite erroneous objectively speaking. It is quite possible that he simply does not know of the concept of co-dominant gene expression or incomplete dominance, or such, and has simply interpreted whatever info he has gotten through his own lack of knowledge.
— In other words, the veracity of anything Liquid says concerning genetics must probably be considered in light of a) his own lack of knowledge of genetics, b) his own personal bone to pick with both Solid and Big Boss, and c) the fact that we cannot guarantee that whatever he has been fed isn't misinformation.
— At no point does Liquid mention the goal of "Les Enfantes Terribles" besides the rant of creating the 'dominant and recessive brothers', if you'll pardon the phrasing, nor does he state that they had direct knowledge of the 'soldier genes' or the effect of each of its alleles at the point of the clonal creation (as doing so would imply the HGP was finished prior to Liquid and Solid's creation in 1976, pre-dating the first human experiments leading to the Genome Soldiers by 25 years). Again, given that what he's saying is on the surface quite erroneous genetically, I personally consider it logical to interpret it as the fact that Liquid probably had little if any idea of the true purpose behind the project or how it worked; again, he is probably interpreting knowledge he must, logically, have acquired second-hand (since he was obviously not alive at the time of the project's creation) through both his own lack of knowledge and whatever spin has been put on the information. He quite possibly automatically leaped to the conclusion that 'dominant = good, recessive = bad'; never quite stopping to think over what how the whole concept works genetically (even if it is obviously possible in the Metal Gear Solid universe).
— Put in layman's terms, Liquid is probably making ignorant statements about something he does not fully understand as a justification for his anger against Solid and Big Boss.
— In fact, if we take the 'recessive=inferior/dominant=superior' dichotomy to be true for all of Big Boss' genes and that the "Les Enfants Terrible" project were somehow able to donate all of the dominant alleles to one clone and the recessive to another (and this is an if scenario that I don't hold to) why would the project, having already gotten all of the dominant alleles out of it, allow a obviously 'inferior' clone to survive? Or why even try to create double-dominant/double recessive clones at all if the goal was simply to create more Big Bosses? The logical answer would be that it obviously had some manner of value to do this — perhaps the project weren't so certain of how 'superior' the dominant alleles in question are, and wanted to check how a double recessive would work — or possibly they weren't simply dominant/recessive and the test was to see how pairs of two identical alleles perform compared to the normal alleles, with incomplete- or co-dominance being the byword instead of 'dominant/recessive'. In either case, of course, Liquid would be a goal for that project, not a disposable by-product, and not a failure.

Anyway, I've digressed. Somewhere half-way through that Wild Mass Guess piece is where the comic comes in. Big boss uses these two pages to talk about his POW on "Les Enfantes Terribles", with the comic author most likely putting together pieces of Liquid's rant with whatever would make for a good story. Big Boss at no point claims any expertise in genetics himself, and unless proven otherwise he was probably more interested in the goings on of a battlefield than the inside of a biology lab — in other words, he probably doesn't know much more than Liquid. He finishes with:

A claim that, at least objectively, correlates with how Liquid's father issues and his knowledge of genetics interlace (how skillfully is more of a subjective term, but objectively nothing said by one of the sources directly opposes the other's). This is where Mantis kicks in — and presumably where you start having problems.

Then, let's establish what Psycho Mantis is saying clearly, in genetics-speak. I'll be discussing their validity below.

— First: 'Dominant gene' is not a valid genetic term. Within genetics, an 'allele' can validly be described as dominant, or recessive, or whatever, but a gene cannot.
— Second: The term 'dominant', within genetics, does not mean 'superior'. Within genetics, 'Dominant' is defined as 'An allele that expresses its phenotypic effect even when heterozygous with a recessive allele; thus, if A is dominant over a, then A/A and A/a have the same phenotype' (Griffiths et al, "Introduction to Genetic Analysis 9th edition" (2008)). Consequently, 'recessive' is defined as 'An allele whose phenotypic effect is not expressed in a heterozygote'. (same).
— Third: The interactions between heterozygous alleles of the same gene are not limited to one being 'dominant' and the other 'recessive': There are other cases, such as for example 'codominance', defined here as 'A situation in which a heterozygote shows the phenotypic effects of both alleles equally' (same).
— Fourth: The term 'clone' and the concept of one of the Snakes possessing all the dominant alleles and the other all the recessive ones are mutually exclusive: Per definition a 'clone' is 'an individual grown from a single somatic cell or cell nucleus and genetically identical to the progenitor cell or organism' (source:http://www.merriam-webster.com/dictionary/clone), which is not the case they possess homozygous alleles in any loci where the progenitor (Big Boss) would be heterozygous.
— As an aside, I'm willing to chalk up the first part of the third statement as extrapolation, but if taken completely straight it is, in fact, incorrect: 'Dominant' and 'recessive' in terms of alleles are terms usually taught at high-school level and entry-level university genetics.

Now, you claim, based on whatever you may choose to source in your rebuttal, that, quote: "The rant says that Liquid is saying the alleles in question are superior because they are dominant. He is not saying this; he says that the dominant alleles are superior because they are the expressed traits of a genetically superior soldier. This is absolutely, entirely accurate. The author's rant is basically beating up a strawman based on a line that only exists inside his head.", presuming that he is here actively using Mantis as a direct outlet for his own opinions and not simply writing an in-character rant for the purposes of either humour or establishing Mantis' character (I'm going to assume he is for the sake of argument).

Thus, the author is incorrect in making the above statement, because given the current context one or more of the above statements is untrue, and in violation of known laws and standards of genetics, as per the Did Not Do The Research trope:

My rebuttal being:

— The first of Mantis' statements is, I believe, beyond reproach. If you have any examples of 'dominant genes' being used in any serious scientific literature about genetics, I motion you put it forward. Otherwise, I'm going to presume there's nothing scientifically wrong with that statement, context or no context.
— The second one is also absolutely correct outside of any context of the Metal Gear Solid world: 'Dominant' and 'recessive' were defined above: If you can quote me a better one, I welcome it. Objectively speaking within the definitions used by the science, 'dominant/recessive' have no correlation with 'superior/inferior'.
— The third statement claims that the interactions of alleles are not limited to dominant/recessive, and that they aren't fully understood yet in Real Life genetics. I don't know if I can effectively quote or source any material that would prove or disprove such a statement, but speaking from my own POW it would seem to me that about the only human genes we do know how function are either those with visible phenotype effects (like hair/eye colour, although those do, as stated, mostly follow a dominant/recessive dualism) or those that inflict genetic diseases, and that this is mostly on a single-gene basis. As for codominance, it is a proven fact, to which I quote the genes for the Major Histocompatability Complex, which are heterozygous codominant (Murphy, Travers, Walport "Janeway's Immunobiology 7th edition" (2008)).
— The fourth statement also seems quite simple, given the definition of 'clone' given above: If there has been an alteration in the genetic codes of Liquid and Solid, they are not genetically identical to Big Boss, and are not his clones, but test-tube babies. It would be incorrect to refer to them as 'clones'.

As for Liquid's rant, at no point does he state that "the dominant alleles are superior because they are the expressed traits of a genetically superior soldier" or that Big Boss' genes were "determined to be superior". Again, the creation of Solid and Liquid predates the Human Genome Project by a good 24 years and the discovery and testing of the 'soldier genes' by about the same time; furthermore, the project would presumably be acting out of a 1976 understanding of genetics, making any insight into the 'genetic superiority' something Liquid would have to be saying with the benefit of hindsight — if his speech can indeed be interpreted to contain anything of the words you describe, which is perhaps more a question of interpretation than anything based on solid fact.

Speaking of what Liquid's speech does contain, Liquid does not mention the word 'allele' once during the entire tirade; perhaps by the same standards this indicates just how little he knows about genetics. Perhaps like me he is simply "bullshitting using Wikipedia" (Wikipedia was, by its own account, launched in 2001; surely enough time for Liquid to chance upon it, and given that the Patriots would likely control the whole thing, probably only helping in giving him entirely the wrong idea). In other words, I argue, and this is my interpretation, that your claim that the author, quote: "makes almost as many mistakes as the games themselves" is based entirely upon a context you have created based on a subjective interpretation of what on the surface is little more than genetic nonsense sprouted by a very irate, non-educated (and possibly misinformed) Liquid Snake. Going by the objective definitions, the only outright faulty statement in Mantis' rant is the part about the middle schoolers, which I for one am willing to chalk up to extrapolation.

As for my statement about co-dominance being, according to you, in discord with Mendelian Principles: This is, of course, another question of definitions and interpretations, so let me clarify by stating that when I said "not everything is as easy to quantify as hair or eye colour, or the colour of pea blossoms used by Mendel when he laid the foundation for genetics", I meant exactly what I meant, as I do not believe (correct me if I'm wrong) that Mendel knew of co-dominance or incomplete dominance when working with his initial pea blossoms. Mendel saw specific traits that were very clearly recessive and dominant in regards to each other; further knowledge in these fields (like with MHC genes and whatnot) have added to this knowledge. But as far as I know none of it has yet to disprove Mendel's basic ideas, which as far as I know are mostly immortalized in his ubiquitous two laws, neither of whom are broken by either game or comic:

That's it for now. Ball is in your court, as they say.

---

A) Metal Gear Solid, the game (or in this case the Twin Snakes remake — I doubt the script was changed that much in that regard)

You would be deeply wrong. There's a lot of major changes [mostly additional stupidity, but it also adds that Snake and Liquid don't have the same colour hair, whereas there is no line to suggest this at all in MGS, suggesting it was a very late change indeed: Meryl even says dark-haired Snake looks "exactly" like Liquid in the original!].

At no point does Liquid mention the goal of "Les Enfantes Terribles" besides the rant of creating the 'dominant and recessive brothers'

Yes he does. It's "To create a phenotype in which all of the dominant genes [alleles] are expressed," or, in layman's terms, to copy Big Boss.

if you'll pardon the phrasing, nor does he state that they had direct knowledge of the 'soldier genes' or the effect of each of its alleles at the point of the clonal creation (as doing so would imply the HGP was finished prior to Liquid and Solid's creation in 1976, pre-dating the first human experiments leading to the Genome Soldiers by 25 years)

No, it wouldn't. They knew Big Boss was a genetically superior soldier at the time or they'd never have even tried to replicate his genetic structure. HGP doesn't have to be complete before they know anything about genetics, we were identifying specific genes and their effects decades before HGP even started.

He quite possibly automatically leaped to the conclusion that 'dominant = good, recessive = bad'; never quite stopping to think over what how the whole concept works genetically (even if it is obviously possible in the Metal Gear Solid universe).

There is no reason to believe this is true and every reason not to; there is a fully objective sense in which Big Boss' expressed traits are superior, because they make a genetically superior soldier. LET knew that, which is why they wanted to make more Big Bosses.

In fact, if we take the 'recessive=inferior/dominant=superior' dichotomy to be true for all of Big Boss' genes and that the "Les Enfants Terrible" project were somehow able to donate all of the dominant alleles to one clone and the recessive to another (and this is an if scenario that I don't hold to) why would the project, having already gotten all of the dominant alleles out of it, allow a obviously 'inferior' clone to survive?

Why kill it? What's the point?

Second: The term 'dominant', within genetics, does not mean 'superior'. Within genetics, 'Dominant' is defined as 'An allele that expresses its phenotypic effect even when heterozygous with a recessive allele; thus, if A is dominant over a, then A/A and A/a have the same phenotype' (Griffiths et al, "Introduction to Genetic Analysis 9th edition" (2008)). Consequently, 'recessive' is defined as 'An allele whose phenotypic effect is not expressed in a heterozygote'. (same).

But in a context where the expressed trait is by an external standard better than the unexpressed [say, a genetically superior soldier], "dominant" does indeed mean "superior." Quoting generic textbook definitions that don't describe external selection doesn't actually change that.

Third: The interactions between heterozygous alleles of the same gene are not limited to one being 'dominant' and the other 'recessive'

That's not what the author has Mantis say, though. He says that the terms "dominant" and "recessive" are wrong. This is completely wrong: "dominant" and "recessive" are not "just terms we teach to middle-schoolers," they are terms that describe a particular type of real relationship between alleles.

The second one is also absolutely correct outside of any context of the Metal Gear Solid world: 'Dominant' and 'recessive' were defined above: If you can quote me a better one, I welcome it. Objectively speaking within the definitions used by the science, 'dominant/recessive' have no correlation with 'superior/inferior'.

No, it's not. You're not taking into account that there is a selective pressure at work here which is judging one allele superior to the other on the basis of whether it is expressed in a particular individual's phenotype or not. There's nothing objective or scientific about it, but Liquid never claims science says dominant alleles are superior, he's saying the project regarded them that way because of it's goal of replicating Big Boss. His speech also outlines that they knew exactly which clone they wanted; hardly surprising, since they wanted expressed traits only the dominant one was going to replicate.

The third statement claims that the interactions of alleles are not limited to dominant/recessive, and that they aren't fully understood yet in Real Life genetics.

Not only not limited to, he's saying that Mendelian heritability does not happen at all, and that all genetic interactions are more complex. This is not doing the research.

As for Liquid's rant, at no point does he state that "the dominant alleles are superior because they are the expressed traits of a genetically superior soldier" or that Big Boss' genes were "determined to be superior".

Actually, he does. The dominant alleles are superior because they're part of Big Boss' phenotype, remember?

Speaking of what Liquid's speech does contain, Liquid does not mention the word 'allele' once during the entire tirade; perhaps by the same standards this indicates just how little he knows about genetics.

It's also possible it's Lost In Translation, though that's rather outside the scope of this discussion.

As for my statement about co-dominance being, according to you, in discord with Mendelian Principles: This is, of course, another question of definitions and interpretations

No, it's not. When we talk about "Mendelian Heritability" we are talking about the simple forms he described. Mantis' speech denies the existence of Mendelian heritability [by claim the dominant and recessive terms Mendelian genetics is defined in terms of to be just terms used to teach children], and claims all genetic interactions are more complex. This is a flat, outright lie, and something nobody with any background in genetics would be stupid enough to suggest. Therefore, the author Did Not Do The Research. It's sadly typical that when learning the more complex theory of a hard science people tend to assume the lower stuff is wrong; you get just as many physics students deciding Newton was wrong because Einstein's theories are more complete.

—- Uknown Troper: My rebuttals, done on a quote-for-quote basis this time:

"You would be deeply wrong. There's a lot of major changes [mostly additional stupidity, but it also adds that Snake and Liquid don't have the same colour hair, whereas there is no line to suggest this at all in MGS, suggesting it was a very late change indeed: Meryl even says dark-haired Snake looks "exactly" like Liquid in the original!]."

Well, If I am deeply wrong, point out where — I expect you to pull any and all relevant information to the field if you feel it helps your case, and to source it properly so it can't be a mistake. If the alterations between the original and the Twin Snakes is an important point in deconstructing my argument, point out where, as long as you can properly prove it.

"Yes he does. It's "To create a phenotype in which all of the dominant genes are expressed," or, in layman's terms, to copy Big Boss."

Which was the rant in question I was alluding to — my apologies for not making that clear. And also, in layman's terms, "To create a phenotype in which all of the dominant genes are expressed" is a self-fulfilling statement, since as you already pointed out purely dominant alleles are always expressed by default. In other words, to the layman, Liquid's words would appear to be nonsensical. The project would by definition succeed with a simple normal clone, without having to mess around with allele-switching, and that Liquid does not appear to realize that lends credence to my theory that he is talking without the benefit of insight into the topic of discussion.

"No, it wouldn't. They knew Big Boss was a genetically superior soldier at the time or they'd never have even tried to replicate his genetic structure. HGP doesn't have to be complete before they know anything about genetics, we were identifying specific genes and their effects decades before HGP even started."

Or it could be simply because he was a superior soldier, genetically or no. Perhaps they wanted to make a nature vs. nurture experiment, use the whole thing as an experiment to test how his alleles fit into mendelevian inheritance. Or just wanted to make more Big Bosses for the purpose of having more of the world's greatest soldier (on a side note, I think the reason why the Genome Soldiers were created is because LET turned out a failure, or simply cost-ineffective, but that's beyond the scope of this discussion). The only thing we know is that they made clones of Big Boss for some reason; the only one's word we have on this being due to his 'genes' is Liquid (and in the Last Days of Foxhound comic, Big Boss), neither of whom make for particularly objective or believable sources: Liquid is mentally unstable and, by comic canon, was deliberately misinformed on the whole subject by Big Boss who is by his own admission both a habitual liar doing it to instil Liquid with neurosis, and not trained in genetics either. Keep in mind that Solid has no knowledge of LET and Liquid does; since Liquid claims that 'father chose me' it implies that he is the source of Liquid's knowledge of LET, an implication the comic treats as explicitly true. Given the timeslot used by the HGP in the real world (1991-2003, 12 years) and that the MGS was finished sometime before 1990 to allow the Patriots to test the newly discovered 'soldier genes' using gene therapy in the Gulf War, that leaves us with a very large time slot between 1976 and 1990 for them to squeeze in the 10-15 years required by the project (possibly longer to take into account more primitive gene sequencing technology), possibly using the lessons first learned by LET as a foundation for mapping said 'soldier genes'.

"There is no reason to believe this is true and every reason not to; there is a fully objective sense in which Big Boss' expressed traits are superior, because they make a genetically superior soldier. LET knew that, which is why they wanted to make more Big Bosses."

How? Explain it. It is a fully objective and proven MGS view that Big Boss is a good soldier, given the man's already impressive history given in the MGS backstory (and later supported by Snake Eater), and there is an objective view they wanted to clone Big Boss since they obviously did it. There is, however, no objective foundation on which to base the assessment that a) Big Boss' genes are all clearly dominant/recessive and b) that the project that created the Snake clones both knew this, and which genes to split up as part of creating the Snake brothers, or even c) if anything Liquid says concerning the gene is true or just misinformation spread by Big Boss, Ocelot and/or the Patriots to provoke him into a conflict with his brother(s).

"Why kill it? What's the point?"

If it had value of some sort, obviously none. If, however, we take Liquid to be true and the goals of LET was "To create a phenotype in which all of the dominant genes are expressed", Liquid is, as he himself says, an unwanted by-product created simply so the project would have an allele donor to create a double dominant, he would be a waste of resources to rear and simply be destroyed. Come to think of it, another fairly silly prospect, in retrospect — if they wanted another bunch of dominant alleles, any one of Big Boss' cells would probably have made an equally suitable donor, meaning that if all Liquid (by his own admission) was there for was as a allele donor he had no reason to exist in the first place. But enough of that.

"But in a context where the expressed trait is by an external standard better than the unexpressed [say, a genetically superior soldier], "dominant" does indeed mean "superior." Quoting generic textbook definitions that don't describe external selection doesn't actually change that."

An external standard that you have created based entirely on the word of Liquid (and Big Boss in the comic), whose veracity as a source I am putting into doubt, and an equally unconfirmed guess on the genetic status of Big Boss' genes and the entire goal of LET, again only based on Liquid. Until otherwise proven, the textbook definition cannot be refuted by Wild Mass Guessing.

"That's not what the author has Mantis say, though. He says that the terms "dominant" and "recessive" are wrong. This is completely wrong: "dominant" and "recessive" are not "just terms we teach to middle-schoolers," they are terms that describe a particular type of real relationship between alleles. (...) Not only not limited to, he's saying that Mendelian heritability does not happen at all, and that all genetic interactions are more complex. This is not doing the research."

I'm going to quote him again: "In reality the interactions of alleles are so complex we don't even understand them yet". Within the context, Mantis appears to be objecting to the usage of such simplified use of genetics to describe a human cloning and allele-switching experiment described to him by Big Boss. He is not in any way saying this is not a true or does not exist, but that basing statements about human cloning on Mendel, without taking into account the 120 years worth of progress done in genetics, obviously does not sit well with him (and probably would not to me either, were I in his position). It's a broad generalized statement that could possibly be worded better, but in itself it is not a proof of lack of research — you'd have to grill the author directly on that.

"Actually, he does. The dominant alleles are superior because they're part of Big Boss' phenotype, remember?"

As I noted, prove it.

"It's also possible it's Lost In Translation, though that's rather outside the scope of this discussion."

No, no, it's perfectly within scope, as it's a core of my statement that Liquid does not know genetics. Now, I am not a linguist, but the japanese word for 'genetic allele' (or just 'allele') appears to be '対立遺伝子' (pronounced 'tairitsuidenshi') whereas the word for 'gene' is 遺伝子 (pronounced 'idenshi'), in other words, the word for 'gene' is a root of the word for 'allele'. I am fairly certain the translators wouldn't make a mistake like that, and if you want to prove otherwise you're going to have to provide the burden of proof.

"No, it's not. When we talk about "Mendelian Heritability" we are talking about the simple forms he described. Mantis' speech denies the existence of Mendelian heritability [by claim the dominant and recessive terms Mendelian genetics is defined in terms of to be just terms used to teach children], and claims all genetic interactions are more complex. This is a flat, outright lie, and something nobody with any background in genetics would be stupid enough to suggest. Therefore, the author Did Not Do The Research. It's sadly typical that when learning the more complex theory of a hard science people tend to assume the lower stuff is wrong; you get just as many physics students deciding Newton was wrong because Einstein's theories are more complete."

Yes, but Einstein's theories build on Newton's — you only teach Newton to begin with to teach people the easy stuff, and then you get to Einstein once you get more proficient at it. It's what Ian Stewart and Jack S. Cohen describe as 'Lies to Children' in Science of the Discworld — start with simple stuff and then branch into the more advanced stuff, building on the massive simplification that the initial knowledge represents with more advanced, filling and accurate knowledge. Mendel chose to work with his pea blossoms because they're simple, and using Mendel and only Mendel and his pure dominant/recessive mendelevian genetics as a core for explaining a human cloning experiment would be like using Newton, and only Newton, to explain wormhole physics or general relativity; it does simply not work on such a simplistic scale in Real Life — and that's not even taking into account the questionable grasp of Mendel's own laws of inheritance Liquid displays when making statements like "to create a phenotype where only the dominant genes are expressed". That is what Mantis is rebelling against. The statement that, again in Real Life, we don't know the full scale of genetic interactions is entirely accurate: Only a few days ago I read a publication concerning that some last fragments of Junk RNA have been found to have some form of function in protein regulation — but we have no real clue as to why.