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March 18

Crossing two humans' DNA

I'm writing a software that takes two raw DNA files in and produces "offspring" DNA from them. The logic it uses currently is roughly:

Choose an offspring sex randomly.
For each of the two inputs:
1. For each chromosome, choose chromatid 1 or 2, and drop the other genotype in each SNP. For instance, if chromatid 2 is chosen for chromosome 3, and SNP rs6801472 has a genotype of AG, then G will be selected from that pair and A will be ignored.
2. If the current parent is male:
  1. Ignore the mitochondrial DNA.
  2. If the offspring is also male, then ignore all X-chromosome SNPs from position 2700000 onwards. (SNPs up to that position seem to have full pairs, rather than single genotypes, in my own male 23andme raw data.)
Combine these new genotypes into pairs for each SNP (except where they are to remain single, e.g. in the X and Y chromosomes and the mtDNA).
If the offspring is male, copy the father's Y chromosome.

Now, given this logic, I think the cross produced should be roughly a 50% match to each parent, but MyHeritage says that my "child" only shares 42.4% of my DNA with me, and therefore guesses that it's my sibling. What could I be doing wrong? M Imtiaz (talk · contribs) 00:55, 18 March 2021 (UTC)[reply]

No comment about why your results are wrong. But if I understand your description correctly, your software comes no where close to matching real world sexual reproduction. Chromosomal crossover during meosis means chromosomes are not inherited as whole units. If SNPs are far away enough on a chromosome, they can be modeled to be inherited independently. In other words, you can't say AG and CT are on the same chromosome therefore if A and C are on one copy of chromosome 3 of the parent and G T on the other, any offspring will either be A C or G T. In reality, there could very well be an equal chance the offspring will be A C, A T, G C, G T. As Centimorgan explains, genetic linkage is complicated so actually modelling this effectively is likely to be difficult, but it would IMO be more accurate to just assume there is no linkage than assume there is complete linkage. Nil Einne (talk) 13:23, 18 March 2021 (UTC)[reply]

Nil Einne, I'm well aware of crossover, and was planning on implementing it later, but I assumed that its effect would be small enough to not matter for now. If it really is more accurate to assume no linkage, then I might just do that.

I also don't think you quite understood what I meant with that description; I'll come around later to clarify once I figure out a better way to word it. Trust me, I'm a bit less of an idiot than I might seem here. M Imtiaz (talk · contribs) 15:32, 18 March 2021 (UTC)[reply]

I surely don't understand what you mean with your SNP manipulations in 2.1, you could probably develop this point further. But I have another question: is this 42.4% result the same for all combinations: mother/male child, mother/female child, father/male child and father/female child? if not, what are the four results? Thanks 2003:F5:6F0A:3500:B082:C125:73D0:C5C9 (talk) 10:40, 20 March 2021 (UTC) Marco PB[reply]

What are biological advantages of human saliva having a lower pH value compared to dog saliva?

Dogs are less likely than humans to have tooth decay due to the very high pH of dog saliva, which prevents an acidic environment from forming and the subsequent demineralization of enamel which would occur.

Source

From wikipedia, I learnt that dog saliva has a higher pH value, so dogs face less dental problems than humans.

What are the biological advantages of human saliva having a lower pH value compared to dog saliva? Rizosome (talk) 01:08, 18 March 2021 (UTC)[reply]

Why are you assuming that the human salivary pH is better? Maybe the advantage is the other way around. Maybe it is more advantageous for a dog to have a higher salivary pH than a human. Or maybe there are advantages for both, based on the different diets and other behaviors of humans and dogs. --Khajidha (talk) 02:48, 18 March 2021 (UTC)[reply]

Some research in other species suggests higher saliva pH correlates with a more acidic diet. (doi:10.1002/ajp.20500) DMacks (talk) 03:48, 18 March 2021 (UTC)[reply]

It is a reasonable assumption that in the course of evolution the advantages and disadvantages of higher or lower saliva acidity in the human species have resulted in a near-optimal balance. Given the disadvantage of tooth decay, one would expect this to be balanced by some advantage of a relatively low pH value. However, the mills of evolution grind slowly, and with the paleolithic diet of early humans, which did not involve ice cream, diet Coke or tomato ketchup but required lots of gnawing, today's diet-induced tooth decay was less of an issue. More importantly, the acidity–basicity of saliva is not a matter of turning a knob; human saliva is a complex mix of many functional substances, some of which are acid, while others are basic.^[1] Considering the functions of these components, the mix may be optimal for the human diet, which differs considerably from the canine diet, and the resulting pH may be more of an accidental side effect. --Lambiam 08:13, 18 March 2021 (UTC)[reply]

Wild speculation. It might be a difference in diet. Humans evolved with an omnivorous diet, where salivary amylase is needed to pre-digest starch. Salivary amylase is active in a neutral or slightly acidic environments. Wolves generally don't eat many plants, so they don't need so much amylase, so can have more alkaline saliva. High pH might have other benefits, say pre-digesting meat, or killing bacteria in old food. AFAIK, caries wasn't really a problem before diets rich in refined sugar were common, so humans haven't evolved to cope with caries. It would be interesting to compare the pH of bears' saliva, as they are omnivores but related to wolves. LongHairedFop (talk) 09:40, 18 March 2021 (UTC)[reply]

Geography

Hi Wiki, please assist, an ex-worker on zoom always had a picture behind him showing coordinates: 52"58 24N 01"07 58W I have done all I can to locate where thus may be but Google has not been of any help.

Thank you — Preceding unsigned comment added by 2A00:23C6:6884:6200:7449:FABC:FAF:3AD9 (talk) 11:35, 18 March 2021 (UTC)[reply]

I suggest you start by looking around York. Dolphin (t) 12:15, 18 March 2021 (UTC)[reply]

If, as I suspect, this is a slight mistake for 52°58'24"N 01°07'58"W, it appears from Google Earth to be within a belt of trees next to an area of grass with soccer goals (though no line markings) just west of Ransom Road in the Mapperley district of Nottingham. {The poster formerly known as 87.81.230.195} 2.221.80.5 (talk) 12:29, 18 March 2021 (UTC)[reply]

Google maps link. --Lambiam 13:00, 18 March 2021 (UTC)[reply]

This is a rather peculiar request, if I may say so. Why has the OP gone to the extent of making a note of these coordinates, while (presumably) never actually asking the ex-worker where they were? That would have been the more straightforward way of going about things. PaleCloudedWhite (talk) 20:09, 18 March 2021 (UTC)[reply]

These zoom calls may have been work meetings with several participants that did not offer a suitable opportunity for dwelling on such non-work-related topics. Perhaps the ex-worker was an avid geocacher. --Lambiam 20:54, 18 March 2021 (UTC)[reply]

That's likely; most other outdoor enthusiasts in the UK use the Ordnance Survey National Grid. Alansplodge (talk) 22:08, 18 March 2021 (UTC)[reply]

A cup of tea

Resolved

When I was growing up, I used to watch Prof Julius Sumner Miller on the TV. I have a couple of his books of puzzles to. One has awlays intrigued me, and I can't remember the answer. I hope clever people here on the Science desk can help. You have made a cup of tea, and you are on the verge of pouring in the milk, when the phone rings. Do you pour in the milk and then answer the phone, or vv? Obviously you want the tea to be as hot as possible when you come back. My gut feeling is you add milk and answer the phone, as the tea wil be closer to room temperature and will have less heat to lose. Thanks! --TrogWoolley (talk) 11:49, 18 March 2021 (UTC)[reply]

I concur with your gut feeling. Heat loss is proportional to the temperature difference between a substance (tea) and its surroundings (see Newton's law of cooling), while the addition of a quantity of colder substance (milk) will cause an immediate temperature drop. Leaving the hot tea undiluted will allow it to lose heat faster followed by an immediate further temperature drop when the milk is added; adding the milk first will immediately drop the overall temperature, but the cooler milked tea will lose heat more slowly.

As to the taste of the resultant tea, I myself am a convinced Prelactarian, but Postlactarians are equally convinced of their righteousness. see Tea in the United Kingdom#Milk and tea which discusses both the taste and the temperature considerations. {The poster formerly known as 87.81.230.195} 2.221.80.5 (talk) 12:42, 18 March 2021 (UTC)[reply]

(ec) Assuming that the cooling is described by Newton's law of cooling, it should not make a difference if the heat transfer coefficient is the same in all cases. If the hot tea is in a cup of china and the milk, just out of the fridge, is in a silverware creamer, the milk will proportionally gain more heat during a waiting period because the silverware has a higher heat transfer coefficient, so then it is better to wait. If it is in a china creamer, or already at room temperature, we need to consider the mechanism behind the heat loss process of the hot cup. The heat is transferred to the air immediately surrounding the cup; since the thermal conductivity of air is low, soon there will be a blanket of hot air around the cup, slowing down the heat transfer. Except for the fact that the hot air rises and is replaced by air at room temperature. The hotter the cup, the faster the air rises, meaning that the effective heat transfer coefficient is higher when the cup is hot. So then it is better to immediately pour the milk so as to bring the coefficient down asap. --Lambiam 12:51, 18 March 2021 (UTC)[reply]

I seem to recall a thread very like this, perhaps even here on this desk (or maybe it was elsewhere). It makes for a fun thought experiment to consider all the minute inputs that are possible. However, for the price of two cups of tea you could just do the experiment for yourself and come up with the "real" answer. Matt Deres (talk) 17:07, 18 March 2021 (UTC)[reply]

You also need a sensitive thermometer with a range of at least up to 85° C, preferably more, and should repeat the experiment a number of times to reduce the effect of experimental error. --Lambiam 20:31, 18 March 2021 (UTC)[reply]

Golly, has it been more than a decade since I had the time to write a simple thermal physics simulation? Regrettably, the server that hosted that simulation is no longer operating, but the source code is available...

In case it isn't self-evident, that code approximates the scenario using Newton's law of cooling. Those who have endured any degree (heh) of engineering education will know that we can add complexity to the problem in many, many, many ways.

Most recently, Incropera, DeWitt, and Bergman's Fundamentals of Heat and Mass Transfer provided me with hours of weekend entertainment, restating the fundamental theories and demonstrating hundreds of variations on the theme of mechanistic engineering approximations to heat transfer between objects of various shapes and fluids of various constituencies. (It was really quite horrible, and even now I find myself waking often in the night, sweats radiating from cold- to hot-, resorting to counting fins to try to return to slumber). The physicist in me wishes that book would spend a little more time on mathematical reanalysis of the generalities after introducing so many special-cases, but ... there is always Stowe's Thermodynamics for the pure physicist in all of us.

Nimur (talk) 18:23, 18 March 2021 (UTC)[reply]

I too remember a similar thread on another venue, probably about 30 years ago. My memory is that it was crucial to include the increase in volume from adding the milk. This means that the liquid rises higher up the mug, increasing the radiative surface. Jmchutchinson (talk) 18:33, 18 March 2021 (UTC)[reply]

Everyone knows that you put the milk in first (i.e. before the tea}. Alansplodge (talk) 22:02, 18 March 2021 (UTC)[reply]

Some people know that you put the milk in never (i.e. not ever). --2603:6081:1C00:1187:C1EB:2F74:40BE:A014 (talk) 23:09, 18 March 2021 (UTC)[reply]

Sugar? Yes. Milk? Yuch. ←Baseball Bugs ^{What's up, Doc?} carrots→ 02:45, 19 March 2021 (UTC)[reply]

Well, at least we don't add harbour water. Alansplodge (talk) 15:10, 20 March 2021 (UTC)[reply]

Thank you for all excellent the replies. I guess for those Prelactarian (What a great term! {The poster formerly known as 87.81.230.195}), it isn't a problem. Being a coffee drinker, it is isn't a real world problem for me either. --TrogWoolley (talk) 12:48, 19 March 2021 (UTC)[reply]