Update: Tioliah has wonderfully expanded upon Emil Karlsson’s excellent post regarding the scientific weaknesses in the idea that the Y chromosome is a broken X chromosome in her comment below. A good read from someone who has forgotten more about mammals than I will ever know!
Update II: Unfortunately Laden has doubled-down on his “it’s right even though it’s wrong” gambit. Ah well, we tried.
Wow. If Laden’s goal was to create discussion and controversy, he’s succeeded on the larger Internet, even if he failed in the discussion at the panel. If there’s any point that’s been reinforced in this, it’s that quite often the answer to a problem (or whether there even is a problem) is almost completely determined by the point of view of the person making the assessment.
If you really want the backstory, you can start here, but as far as I can tell, the issues center around two words used in two sentences.
The first, a joke by Heina Dadabhoy, is that the Y chromosome is a broken X chromosome. I didn’t give any thought to it because it was (to me) an obvious laugh line, and she came out and on Twitter specifically said it was a joke. So to me, that horse had already been beaten to death, and I didn’t want to add to the drama, and I had forgotten about it. Note the past perfect tense.
The second is the word “damaged” in the sentence “You know, the male brain is a female brain damaged by testosterone in various stages in it’s life,” which I took issue with here there, and everywhere (including in the aforementioned blog post I linked for context).
My position is fairly basic on this: to use the word “broken” and “damaged” is to stray from describing naturally-evolving processes (meaning not guided by conscious motivation). In both cases, you’re either implying (not intentionally, linguistically) that there is an inherent template a la Platonic Forms that these “damaged” or “broken” things are not properly adhering to, or that there is some perspective from which such a value judgement can be made. To me, this is a big problem because you’re feeding a natural habit of human beings (to assume that those spots in the dark are eyes, and that those eyes are looking at you) that is backed by the evolutionary reward of your ancestors’ hyper-vigilance leading to you eventually being born. This isn’t to say that being careful of predator animals is a bad thing, just that what is a survival skill in the wild (or in a back alley) is delusion and plain wooly thinking in science.
I understand the point Laden was trying to make, and I’ve already responded to it (and have no desire to hash it out further, though I still can’t recommend Emil Karlsson’s post at Debunking Denialism enough). I though I was pretty much done with this topic until yesterday.
Enter a tweeter named @HorsePheathers, who apparently was talking with sofiarune or Emil (or both), defending the idea that “broken” was appropriate when referring to the Y chromosome. I held back for a long time to let those with real biology experience have it out with them, and when sofiarune threw up her hands, I jumped in from a linguistic perspective. It turns out that HorsePheathers may be a science writer, and we had a relatively spirited discussion about the subject.
I’m going to lay out what I understand his position to be and a response, because I’m sick of having this discussion in 140-character bites. This list is not exhaustive, but this is all I can remember off-the-cuff. The (source) links are there for reference, not because I have any pretensions of whatever.
But first: I was wrong (either factually or morally) about the following:
1. I shouldn’t have used the word “misinformation” when describing what he was doing, when I meant “oversimplified information for the convenience of the writer, the preference of the non-scientifically educated editor, and the least-common-denominator-reader.”
2. At one point I used the word gene where I meant chromosome.
3. I shouldn’t have resorted to two personal attacks, and for that I apologize.
With that having been said, his main avenue of arguments were (in no particular order, again not a comprehensive list. Copy/paste from twitter where possible because I’m lazy):
1. The Y lost functionality in the transition from just another X chromosome, the loss of functionality and the other introduced problems (recessive genes located on the corresponding X chromosome being more likely to be expressed, etc) is a greater loss than the gain of our sex-selection mechanism, etc., therefore “broken” is an acceptable term for lost functionality and increased problems. (too many to source and I’m lazy)
2. Variants of “Back into the IT context: if you’re trying to teach a user a new piece of software and it requires a minimum csh use expounding on the capabilities of ls beyond dir just gets in the way. There’s room later to expand on the knowledge.” (source 1 and source 2) and “Or do you think a first grader is ready for the specifics of genetic coalescence rather than “populations change over time”?” (source)
3. From a biologist he had dinner with last night: “Also from her, paraphrased: We’re dealing w’ folks who haven’t a clue how water boils, & you lot are splitting hairs on this?” (source) “The entire process of education is a series of just such simplifications that are expanded on or refined in future lessons” (source) and “Or do you think a first grader is ready for the specifics of genetic coalescence rather than “populations change over time”?” (source) “Who is talking about attributing motivation to genetic processes? I’m certainly not.” (source)
4. “No, I’m saying that “just good enough” applies here as well as in biology. Asymptotic approach, remember?” (source)
As for your biologist friend, I don’t know whether or not you presented the entire conversation, or whether you simply relayed it verbally, so I’ll take all that with a grain of salt. Given the rough-and-tumble tone of our discussion (and even more so, the tone of the larger discussion), I’m not taking it personally.
I do not apologize for using “quite well,” as snark is the native language of the Internet. I will emphasize that “good enough to pass on your genes more successfully than those who are competing for your ecological niche” is the only measure of “quite well” or even “good enough” in an evolutionary context (as you noted above)
I’ll rephrase my initial critique one more time before diving into the individual arguments: “broken” and “damaged” imply an alternate state that would be “not broken” in which lost function would be restored. The Y chromosome does what it does and mammals are breeding like rabbits (as their selection strategy permits), so I don’t see a way to un-break it that would result in an improvement of its function. Using the words “derived from,” “a variant of,” etc. are not at all objectionable to me, because they do not carry this implication. To use an example I tried to use on twitter but failed to by reason of character limit, an ostrich wing is not a “broken” wing because it doesn’t allow ostriches to fly, it aids the bird’s balance and direction control via both weight distribution and airflow manipulation. It does what it does, not what another bird’s wing does. Nor is an ostrich wing a “broken” foot: even though it’s descended from a forelimb, that was then, and this is now.
Now to the individual arguments:
1. We went back and forth a few times over this one, and my primary critique of it is the ostrich example. A secondary critique would be that even valuing a larger number of functional alleles over a smaller number is a human value judgement, and can be argued against. A smaller number of functions could be limited to important, highly conserved functions that are now performed more robustly. According to some criteria, that might be considered better than simply having more functions. As to recessive sex-linked genetic disorders that the Y chromosome lacks the ability to mask, it could be argued that the Y chromosome acts as a reproductive filter. Recessive genes that carry negative traits that would otherwise be passed on (only to express themselves at some later date) are immediately expressed in males, which are therefore less likely to reproduce, lessening the presence of that trait in the population. The argument from functionality and errors alone cuts both ways.
2. This is a four-part problem here. When you compare ls and dir, the analogy is better suited to convergent evolution (wings on both birds and bats, for example) than derivation. The second (which I’ll go over in more detail later), is that you’re introducing a misconception through outright error rather than oversimplification that would need to be corrected (MS-DOS was made for a much less complex environment rather than a server environment, and much of the functionality in ls that is not present in dir is present in the Windows GUI, which is an entirely different critter). The last point, which comes into play if you accept the analogy as intended, could be summed up as: is it really appropriate to introduce the material at that point if you have to oversimplify it to the degree where any error is essentially taking two steps back generally so you can one step forward on that precise subject? More on that in the next point.
3. This is precisely my concern, and why I think science writing is under-paid, under-valued, and poorly done by journalists who phone it in when they’d rather be doing political and social stories that get them attention and access to people with power and money. Essentially, in a nation where so many people believe in literal angels, that an oddly-shaped knot on a tree is a manifestation of the Virgin Mary, that the Earth and all its creatures were created intentionally, and that a personal god might give you a winning lottery ticket if you ask hard enough, anything that even hints of animism in science discussion makes my hair stand up on end. This is an opening that has been exploited in school boards for years, and (along with fundamental misunderstandings such as what “theory” means in a scientific sense) results in a cry to “teach the controversy.” Language matters in these fights, and I get reminded of that every day, whether I’m reading the news from Texas or (in the past, since I’m no longer supporting end users) trying to communicate with someone who is deeply convinced their computer hates them. This would be the vast majority of my investment in this topic, because I see first-hand the consequences of bad science education.
4. Regarding #4, that “good enough” is good enough in science writing as it is in evolution, I disagree completely, especially in basic science education. The recurrent laryngeal nerve is good enough because the vast majority of us are capable of speaking (therefore it’s functioning), but it’s necessarily the way it is because it’s the product of evolution. Science education as a whole is the product of the conscious actions of millions of people. When we are buried down in this unglamorous level of what can feel like drudgery, it’s easy to forget that foundational steps are the most lasting, especially when correcting errors. The first example that comes to mind is building a house, but any structure (from a bridge to a house of cards) is appropriate for this as well. The earlier and the more foundational the mistake, the more problematic the eventual failure that occurs. This is not just true of buildings, but also of beliefs. If it weren’t true of how our brain works (and I’ll be happy to dig up papers when I have a moment), then everything from the concept of “situated freedoms” in Existentialism to “path dependence” in decision theory would have no weight. Add to that the social embarrassment associated with being seen making a mistake, and the bar becomes increasingly higher for each subsequent educator after you until and unless the student learns and applies the skills associated with rational self-correction.
It really is very easy to give into the demand for complete-sounding information from someone who has no information on a subject, but I’ve never found it to be genuinely useful for anything other than either intentional sabotage or escape from a conversation or task that I don’t want to be involved in any more. This makes me unpopular, but there are usually fewer loose ends for me to deal with later on.
I’ll have a glass of Laphroaig Triple-Wood later on to celebrate the end of the Twitter fight. :D
My Two Cents (Or All the Reasons Why I Think it’s Wrong to Call the Y Chromosome “Broken”)
Thank you, Badger, for such a well-written post! I followed some of the tweets both you and Sofiarune had with Horsepheathers, and there are a few more things I feel need mentioning. This comment deals mostly with your first point and the arguments that were made in favour of referring to the Y as a “broken” chromosome:
“1. The Y lost functionality in the transition from just another X chromosome, the loss of functionality and the other introduced problems (recessive genes located on the corresponding X chromosome being more likely to be expressed, etc) is a greater loss than the gain of our sex-selection mechanism, etc., therefore “broken” is an acceptable term for lost functionality and increased problems. (too many to source and I’m lazy)”
Okay, here we go (and I apologize for this being a few days late!)
1. Males are more prone to expressing deleterious X-linked recessive alleles
First, I think Emil Karlsson did a good job going over the basic genetics of the sex chromosomes here. http://debunkingdenialism.com/2012/07/22/some-falsehoods-about-the-y-chromosome-and-male-brains/
From what I’ve seen, one of the reasons being used to justify calling the Y chromosome “broken” is that XY individuals are more likely to express X-linked recessive disorders because they do not have a second X potentially acting as a buffer against recessive allele expression. Among other things, Emil points out in his post that where X-linked disorders are concerned, it’s the X chromosome with the “broken” gene (recessive deleterious allele), not the Y. This is made all the more apparent when you consider that XX individuals who are homozygous for the offending gene (both X’s possess the deleterious allele) will also express the associated disorder, as will individuals with Turner’s Syndrome (X0 – only one X chromosome). In both of these cases, X-linked disorders are being expressed in individuals without a Y chromosome. As such, it seems a stretch to me to include the likelihood of expressing X-linked disorders among criteria for judging the Y to be broken.
2. The Y is derived from the X chromosome, so calling it a “broken X” is acceptable
Second, I keep seeing something along the lines of this: “The Y chromosome evolved from/used to be an X chromosome”. This is being used to justify comparing the Y to the X (e.g. The Y can be considered “broken” because of the amount of function loss it underwent relative to its prior X state). This is not true. Research has shown rather conclusively that the mammalian X and Y chromosomes each evolved from an ancestral autosome (non-sex chromosome). Recent work on the platypus genome has revealed that conserved (important) genes on the therian X and Y chromosomes have orthologs on one of the platypus’ autosomes (chromosome 6). Orthologs are homologous genes in separate species that share a common ancestor gene in an ancestral species. What this means is that our X and Y chromosomes evolved from an autosomal pair in an ancestral mammal that existed just after the monotremes and therians (non-egg laying mammals) diverged, about 166 million years ago. http://www.ncbi.nlm.nih.gov/pubmed/18463302
Incidentally, the platypus actually has 5 pairs of sex chromosomes that share many similarities with bird sex chromosomes, which suggests that prior to the evolution of our X and Y, mammals had a bird-like sex determination system. http://www.nature.com/nature/journal/v453/n7192/full/nature06936.html
I suppose you might say, in this context, that both the X and Y are “broken” versions of the autosomes they are derived from, no? After all, we wouldn’t have any of our modern X OR Y-linked disorders if we’d kept our ancestral bird-like sex determining system.
So where did the misconception about the Y evolving from the X come from? Well, even though both X and Y evolved from an autosomal pair, a translocation event (a mutation event during which a section of one chromosome is inserted into another) is thought to have isolated some male sex-determining genes on one member of that autosomal pair first. This would then have become the ancestral Y chromosome (and the other member of the pair would then be the ancestral X). Now, if you compare the modern X and Y to the other mammalian autosomes, the Y certainly stands out as atypical, but that is only after an accumulation of evolutionary changes. The ancestral Y would have been much more comparable in its behavior to the other autosomes, including the ancestral X. So in that sense, the common ancestor gene of the X and Y would have more closely resembled the modern X than the modern Y. This does not mean, however, that the Y evolved from X (just as humans did not evolve from the coelacanth, even though the latter much more closely resembles the common ancestor we share with it). Additionally, orthologs of the modern therian X were once thought to be dispersed on the platypus’ sex chromosomes, suggesting that our X and Y evolved from ancestral sex-determining (and X-like) chromosmes, not autosomes.
The initial translocation event responsible for initiating X/Y divergence was then followed by a gradual series of others that continued to isolate male sex determining genes and genes beneficial to males (but harmful to females) on the Y. One study suggests there were 4 key translocation events throughout mammalian evolutionary history, though the time estimates here have since been shown to likely be off http://www.ncbi.nlm.nih.gov/pubmed/10542153.
These changes were selected for as the increased isolation of sex-determining genes on each chromosome made recombination more harmful than advantageous. In other words, in this evolutionary context, the development of the Y’s inability to recombine with the X was BENEFICIAL. Has this since resulted in problems because now the Y is not as effective at exposing its genes to natural selection? Yes, but if the Y did not lose alot of its ability to recombine, we would not have our modern sex-determination system at all. Again, I do not see this as an acceptable criterion by which to judge the Y “broken”.
3. The Y is shrinking and it can’t recombine with the X
Emil wrote about the disappearing Y (and its possible debunking), and Y self-recombination in his post, so I won’t rehash that here.
4. The Y has a much higher mutation rate relative to the X and most other chromosomes
A final criterion by which the Y could possibly be judged “broken” is its higher mutation rate relative to the other chromosomes. Here, though, I’d still argue this judgment is not correct because this high mutation rate arises primarily from the Y’s physiological environment (oxidative nature of the testes) and a high rate of sperm division, not necessarily the Y itself.
Overall, these costs associated with the Y are, like all other biological “costs” from exploding appendices to herniated vertebral discs, outweighed by the advantages they have provided along our evolutionary history (the appendix once allowed our ancestors to digest cellulose, and back problems are the price we pay for walking upright :-P). Calling any of these structures “broken” seems to me like a gross discounting of their evolutionary contexts.
5. But what if….
Some researchers think that, even in spite of self-recombination, the Y is still heading towards disappearance in the future. http://www.publish.csiro.au/?paper=RD03096 .
However, it’s highly unlikely this will lead to the extinction of men or an all-female society or some such equivalent. Male sex determining genes will more likely be translocated elsewhere, as has already happened in some rodents for example: http://www.ncbi.nlm.nih.gov/pubmed/12900579
In fact, the SRY gene on the Y chromosome (the gene responsible for male sex determination and which is highly involved in embryonic development), CAN be recombined onto the X in humans. This results in a rare condition referred to as the XX male. However, these individuals are sterile due to a lack of other genes involved in sperm production http://www.healthline.com/galecontent/xx-male-syndrome#1.
Nevertheless, this shows that translocation of male determining genes onto other chromosomes is possible, even in humans.
How the Y will fare in future is unclear, but if it is headed on a trajectory towards oblivion, that still does not make it “broken” because we are assigning value to having it stick around.
6. Well, function loss was STILL involved in the Y chromosome’s evolution, so “broken” is an acceptable term on that basis.
A final point: using loss of function to judge a chromosome (or more appropriately, a gene) “broken” might only be acceptable in an immediate, not in an historical context.
A rare event/mutation/translocation could result in a “broken” gene if the new allele caused an impairment of function (was deleterious). BUT, what if this impairment of function turned out not to be an issue for the organisms in question due to recent occupation of a new environment? Take for example, the loss of function of one of the cone pigment genes in cetaceans and echolocating bats, “impairing” their colour perception in environments where they rely heavily on sound. The impairment in this context turns out just to be the loss of an unnecessary gene. A mutation that causes a loss of original function may even turn out to result or enable the gain of new functions that turn out to be an advantage. Functionality itself is relative in an evolutionary context.
Even in a non-historical/evolutionary context, using words like “damaged” and “broken” to describe uncommon alleles can have social consequences. For example, would using “broken” be appropriate in describing SRY alleles that are involved in certain syndromes such as androgen insensitivity, a condition that affects many intersex people? What are the social ramifications of using the word “broken” to describe the genetics of these people? Are intersex people with an atypically functioning SRY gene “broken”? Are their SRY genes “broken” for causing androgen insensitivity? Can we truly say this given the (supposedly) progressive nature of our modern society? This is a case where use of the word “broken” might be arguably more appropriate, and yet the value-laden judgment implied in the word is STILL potentially destructive.
Ah, but what about the trickiness of writing science articles for the lay-public who do not have the benefit of reading my rambly rant of an essay? “Broken” is an exciting term that people can intuitively relate to. It captures interest better than a more accurate word like “specialized”. Role on a second comment dealing with Badger’s point #3…. Maybe…. in another few days :-P
As a final disclaimer, I apologize in advance if I have misunderstood (and thus misrepresented) anyone’s opinions on this matter.
:O Thank you!!
And thank you for the compliment, I did the best I could with the comparatively small amount of knowledge I had to work with (which you remedied with your comment, and which I’ll be noting at the top of the post!).
Wow, this is a great comment!
Isn’t it the case that, in the bird-like system of sex determination, the female actually has the Y-like chromosome (termed W) ? I’ve also read (forget where) that if one removes the ovaries of, say, a peahen, she’ll begin to develop bright plumage similar to that of the males – meaning that males are the “default” approach for birds, opposite of mammals. It seems more or less “random,” if you will, that females are XX and males XY in mammals.