Relatedness is relative: How can I be 85% genetically similar to my mom, but only related to her by half?

First of all, no. I am not the lovechild of star-crossed siblings, or even cousins, or even second cousins. 

This is a gee-whiz kind of post. But the issues are not insignificant.

Hear me out with the background, first, before I get to the part where my eyes bug out of my head and I pull out my kid's Crayola box and start drawing.

If you've learned about sociobiology, or evolutionary psychology, or inclusive fitness, or kin selection, or the evolution of cooperation and even "altruism," or if you've read The Selfish Gene, or if you've been able to follow the debate about levels of selection (which you can peek at here)...

... then you've heard that you're related to your parents by 1/2, to your siblings by 1/2 as well, to your grandparents and grandchildren by 1/4, to your aunts and uncles and nieces and nephews by 1/4 as well, and to your first cousins by 1/8 and so on and so forth.  (Here's some more information.)

So, for example. For evolution (read: adaptationism) to explain how cooperative social behavior could be adaptive in the genetic sense, we use the following logic provided by Bill Hamilton, which became known as "Hamilton's Rule": 

The cost to your cooperation or your prosocial behavior (C) must be less than its benefit to you (B), reproductively speaking, relative to how genetically related (r) you are to the individual with whom you're cooperating. That could have come out smoother. Oh, here you go:

C < rB, or B > C/r

If you're helping out your identical genetic twin (r=1.0), then as long as the benefit to you is greater than the cost, it's adaptive.

C < B, or B > C

If you're helping out your daughter (r = 0.5) then as long as the benefit to you is greater than twice the cost, it's adaptive.

C < (1/2)B, or B > 2C

So already, the adaptive risk to helping out your daughter or your brother is quite higher. And it's even harder to justify the cooperation between individuals and their sibs' kids, and grandkids, especially ESPECIALLY non-kin. But, of course creatures do it! And so do we.

As relatedness gets more distant and distant, we go from 2 times the cost, to 4 times, 8 times, 16, 32, 64 etc... You can see why people like to say "the math falls away" or "drops off" at first or second cousins when they're explaining where the arbitrary line of genetic "kin" is drawn.  If you offer up a curious, "we're all related, we're all kin," someone out of this school of thought that's focused on explaining the evolution of and genes for social behavior may clue you in by circumscribing "kin" as the members of a group that are r = 1/8 or r = 1/16 but usually not less related than that.

This has long bothered me because we're all genetically related and so much cooperation beyond close kin is happening. And it's been hard for me, as someone who sees everything as connected, to read text after text supporting "kin selection" and "kin recognition" (knowing who to be kind to and who to avoid bleeping), to get past the fact that we're arbitrarily deciding what is "kin" and it seems to be for convenience. I'm not doubting that cooperation is important for evolutionary reasons. Quite the contrary! It's just that why is there so much math, based in so many potentially unnecessary assumptions about genes for behavior, gracing so many pages of scientific literature for explaining it or underscoring its importance? 

(It could just be that as an outsider and a non-expert I just don't understand enough of it and if I only did, I wouldn't be gracing this blog with my questions. But let's get back to my reason for posting anyway because it's potentially useful.)

Right. So. Even for folks who aren't part of evolution's academic endeavor, it's obvious to most that we're one half dad and one half mom. The sperm carries one half of a genome, the egg another, and together they make a whole genome which becomes the kid. Voila!

There's even an adorable "Biologist's Mother's Day" song about how we've got half our moms' genome... 

... but there's biology above and beyond the genes we get from mom (and not from dad). And that song is great for teaching us that the rest of the egg and the gestational experience in utero provide so much more to the development of the soon-to-be new human. So "slightly more than half of everything" is thanks to our mothers. Aw!

But, genetically, the mainstream idea is still that we're 50% our mom. 

I teach very basic genetics because I teach evolution and anthropology.And I'm not (usually) a dummy.* I get it. It's a fact! I'm half, genetically, my mom and I'm also half my dad. 

r = 0.5

Okay! But, given these facts about relatedness and how it's imagined in evolutionary biology, facts that I never ever questioned, I hope you can see why this report from 23andMe (personal genomics enterprise) blew my mind:

Percent similarity to Holly Dunsworth over 536070 SNPs (single nucleotide polymorphisms or, effectively/rather, a subset of known variants in the genome; Click on the image to enlarge).
I am 85% like my mom and I am at least 76% like my students and friends who are sharing with me on 23andMe. Names of comparisons have been redacted. As far as I know, this kind of report is no longer offered by 23andMe. I spat back in 2011/12 and the platform has evolved since.

Okay, first of all, it is a huge relief that, of all the people I'm sharing with on 23andMe, the one who squeezed me out of her body is the most genetically similar to me. Science works.

But that number there, with my mother, it is not 50%. It's quite a bit bigger than that. It says I'm over 85% the same as her.

What's more, I am also very similar to every single person I'm sharing with on the site, including example accounts from halfway around the world. Everyone is at least 60-ish% genetically similar to me, according to 23andMe. I know we're all "cousins," but my actual cousins are supposed to be 1/8th according to evolutionary biology. How can my mom be related to me by only one half? How can my actual cousins be only an eighth (which is 12.5%)? 

What is up with evolutionary biology and this whole "r" thing?

Hi. Here is where, if they weren't already, people just got really annoyed with me. Evolutionary biology's "relatedness" or "r" is not the same as genetic similarity like that reported by 23andMe.

Okay!

But why not? 

Let me help unpack the 85% genetic similarity with my mom. Remember, it's not because I'm inbred (which you have to take my word for, but notice that most everyone on there is over 70% genetically similar to me so...).

It's because my mom and dad, just like any two humans, share a lot in common genetically. Some of the alleles that I inherited from my dad are alleles that my mom inherited from her parents. So, not only is everything I got from her (50%) similar to her, but so are many of the parts that I got from my dad. 

Let me get out my kid's arts supplies.

Here is a pretty common view of relatedness, genetically. In our imagination, parents are not related (r = 0) which can lead our imagination to think that their alleles are distinct. Here there are four distinct alleles/variants that could be passed onto offspring, with each offspring only getting one from mom and one from dad. In this case, the sperm carrying the orange variant and the egg with the blue variant made the baby.

1. (Please, if you're horrified by the "r" business in these figures, read the post for explanation.)

But few genes have four known alleles, at least not four that exist at an appreciable frequency. Some could have three. What does that look like? 

The green allele doesn't exist in the next example. As a result of there being only three variants for this gene or locus, mom and dad must share at least one allele, minimum. That means, they look related and that means that, depending on which egg and sperm make the kid, the kid could be more related to mom than to dad. 

2. (Please, if you're horrified by the "r" business in these figures, read the post for explanation.)

Now here's where people who know more than I do about these things say that the kid is not more related to mom than dad because she got only one allele from mom and that keeps her at r = 0.5. 

Well, that's just insane. What does it matter whether she got the allele from mom or dad? I thought genes were selfish? (Sorry, for the outburst.)

Again, I realize I'm annoying people and probably much worse--like stomping all over theory and knowledge and science--by mixing up the different concepts of genetic similarity (e.g. 50%) with "r" (e.g. 0.5) and horribly misunderstanding all the nuance (and debate) about "r," but I'm doing it because I'm desperately trying to know why these two related ideas are, in fact, distinct. 

One last pathetic cartoon. 

In this third example, as is common in the genome, there are only two alleles/variants in existence (at an appreciable frequency, so not accounting for constant accumulation of de novo variation). An example of such a gene with only two known alleles is the "earwax gene" ABCC11 (there's a wet/waxy allele and dry/crumbly one). Here, the two alleles are orange and blue. Most humans in the species will have at least one allele in common with their mate for a gene with two alleles, and it's not because most humans are inbred, unless we want to redefine inbreeding to include very distant relatives (aside: which may be how the term is used by experts). 

3. (Please, if you're horrified by the "r" business in these figures, read the post for explanation.)

But as a result of the chance segregation of either the blue or orange allele into each of the gametes, two people with the same genotype can make a kid with the same genotype. 

And of course, making a kid with your same genotype is the only possible outcome if you and your mate are both homozygous (i.e. where both copies are of the same variant so that leaves no chance for variation in offspring unless there is a new mutation). 

So, I wandered a little bit away from my point with these drawings, but I had to because I wanted to get down from where my imagination has me (us?) with "r" versus how things really are with reproduction. We are baby-making with vastly similar genomes to ours, so we are making babies with vastly similar genomes to ours. 

So, I do see why biology says I'm related to my mom by one half. But, on the other hand, what does it matter if I got the thing I have in common with my mom from my mom or whether I got it from my dad? Because I got it. Period. It lives. Period. 

[Inserted graf January 20, '17] Saying it matters where I got the similarity to my mom keeps us at r = 0.5. Saying it matters only that I inherited DNA like hers keeps us always, all of us, at r > 0.5 with our parents and our kids because any two babymakers share much of their genome.

And the fact that this (see 2 and 3) happens so often is why I'm a lot more than 50% genetically like my mom, and the same can be said about my genetic similarity to my dad without him even spitting for 23andMe. 

So, here we are. I don't understand why our relatedness to one another, based on genetic similarity, is not "r."

I hope it's for really beautifully logical reasons and not something political. 

Because...

If "r" was defined by genetic similarity, then would cooperating with my 76% genetically similar students and friends be more adaptive than the credit I currently get from evolutionary biology for cooperating with my own flesh and blood son? 

If "r" was defined by genetic similarity, then could we use the power of math and theoretical biology to encourage broader cooperation among humans beyond their close kin? 

So many questions.

Maybe I should re-learn the math and learn all the other math.

Nah. Not myself. At least, it wouldn't come fast enough for my appetite. Maybe someone who already knows the math could leave a comment and we could go from there... 

And it would be worth it, you know, because despite my relatively weaker math skills, I bet we're more than 50% genetically similar.

*from 23andMe: "You have 321 Neanderthal variants. You have more Neanderthal variants than 96% of 23andMe customers."

 Old bottles are a great way of displaying single flower stems; in this case I've chosen some vintage fabric flowers and added a touch of ribbon. I put these into the shop today as my way of encouraging spring to arrive. The daffodils are already out and the first snowdrops. Is it really only two weeks since New Year?

Amerika'da Yeni Yıl ve Kar

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Aşk Amerika'da yaşanıyor güzelim. Amerika bana, ben Amerika'ya özelim...

Höff resmen anlatım bozukluğu var bu şarkıda. 

Güneyde kış yok dediydiler, kendimi kar bekleyen İzmirli psikolojisine hazırlamıştım. Hakkaten kış bir geliyor, bir gidiyor buralara, daha çok bahar serinliği gibi. Hele kar hiç beklemeyin dediydiler. İncecik yağar. 

Ay bir yağdı. Gerçekten bir gün yağdı. Üç, dört gün kaldı. Biz de bulunca suyunu çıkardık. 

Kapılarımıza hava -1 derece olacak diye bir gün önceden yazı bıraktılar. Suların donmaması için önlemler yazıyordu. Şu üstteki kadar kar yağdı. Bütün gün kar araçları yolları temizledi. 

Hepimizin hayatını temsilen. Ama çok tatlış oldu ya! Kısa film dalında bütün kategorilere adayım...

⭐ 

Yılbaşı zamanı evleri muazzam ışıklandırdılar. Kendi inançları, kendi bayramları sonuçta.

Baktıkça bizim bayramlarımızın ne kadar sönük geçtiğini düşünüp üzüldüm. Bayramlar bizde akraba ziyaretlerine, zoraki ev gezmelerine veya tatil hayallerine sıkışmış durumda. 

 Oysa Osmanlı'da böyle miydi bayram eğlenceleri? 

Kabul edelim nerde o eski bayramlar derken bile bu zorakiliği kast ediyoruz aslında. Acilen kültürümüze uygun şekilde güncellememiz gerekiyor bazı şeyleri. Çok şeyleri. Zamanla anlatırım inşallah. 

Burda hemen her evin yanında yöresinde dekoratif süsler var. Geçenlerde boş bir eve bakmaya gittik. Evin önündeki porselen süsleri, heykelleri almamışlar, öylece duruyor. Kimse çalmıyor. Ya bizde olsa? 

Neyse...

Bakalım evleri nasıl süslemişler...

Sevgiler canlar 

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İç Ses - 29

Anlamak ve anlaşmak arasındaki boşluğa sıkışan iç sıkıntıları yazmıştım bir köşeye şimdi yazmak için oturunca beyaz ışığın karşısına aklıma geldi. Anlaşmaya yetmeyen anlamaların ruhumuzun üzerinden geçip gittiği dönemin adı yetişkinlik sanırım. Olgunluk denen ömrün arka bahçesi dönemine geldiğimde ya anlama çabasından ya da anlaşmaktan vazgeçmiş olmayı umuyorum.

Maddi hırslara kapılıp bir kazanmak telaşı ile ömür tüketme üzerine programlı biri olmadığım için, hayallerime kapılıp, dünya denen yeri anlama telaşı ile ömür tüketiyorum. Bir huzur dönemi olacaktır illa ki değil mi? Olur olur ya bence :)

Yaşarken ve hayat sağımdan solumdan akarken içimde bazen gerçek bir dinginlikle biraz sabır bak zamanla nasıl da haklı çıkacağım dediğim anlar, hisler; bazen hiç bitmeyecekmiş gibi hissettiğim, hep hataya teşne bir çömezlik…  

Belki kardeşle yaşamanın verdiği idare etme refleksi, belki yaşlıyla büyümenin verdiği ihtiyar bir kabullenişle duvarsız, yalansız, apaçık devam etme arzusu.

Ananem insanın geçinmeye gönlü olcak derdi, sağlığında kulağıma yerleşen ve her geçen gün ne kadar da haklı olduğunu bir kere daha fark ettiğim cümlelerden. Geçinmekten kast ettiği anlaşmak, devam etmek yani.

 Geçinmeye niyetim var benim hayatla da umutla da, sık sık içimin huzursuzluğu ile ruhumu duvardan duvara vurmalarımın kaynağı anlaşılamayan çocuk telaşı sanırım.

Anlaşılamamaya dair duyduğum çömez kaygı.  

Anlıyorum aslında diye başlayan cümlelerin gönlü tatmin ettiği günler diliyorum kendime, ne diyeyim daha başka.  

St Ives in Winter

 J and I took a little trip to St. Ives yesterday. It's somewhere I love to come in wintertime when the place is quiet and subdued. 

The boats are pulled up and there's only a couple of walkers on the beach, along with these cheeky chaps.....

After searching on the shoreline for sea-glass and shells we mooched up the high street looking in the shop windows. First the Cornish designer-maker Poppy Treffry......

and then some clothes stores.....

 and the best gallery in town, 'The New Craftsman'.

Finally a nice cup of hot chocolate and a slice of tiffin before heading home. Just nice!

Hint Filmi: Raavanan

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    Nasıl desem bir tuhaf film. Tuhaf  şekilde çok beğendim.
  Aishwarya Rai ve Vikram rollerine çok yakışmışlar. Aynı film aynı yıl, Aishwarya Rai aynı kalarak başka bir versiyonu da çekilmiş. İkisini de izledim. Raavanan çok daha güzel geldi bana.
      Filmi hintfilmiizle sitesinden izledim.

   Yer, zaman, olay, kişiler... Hepsi cuk. Sonu böyle olmamalıydı türünden ama filme yakışan da oymuş gibi. Arada köprülü aksiyon sahnesi içinizi hoplatabilir. 

  Konu özetle ve spoilersız şöyle; olağanüstü manzaralar içinde, emniyet müdürünün muhteşem karısı, değişik garip bir adam tarafından kaçırılıyor. Elbette bir amacı var ve siz film boyunca adamımız Veera gibi kaşlarınızı çatıp, dişlerinizi sıkıyorsunuz.
    Ama sonu niye öyle oldu ya! Bollywood yapma bunu bize! (Kendimi acilen dutmalıyım)... 

     Öyle ortalarda dolaşan bir film değil bu. Çoğunuz duymamışsınızdır belki. Ben de rastlamamıştım daha önce.
   Bir gün içinde  Maan Geet dizisinde bir şarkıya vurulmam, internette aratmam ve aşağıdaki klibine ulaşmam beni filme götürdü.

    Videoyu izleyince ne demek istediğimi anlayacaksınız. E o zaman iyi seyirler! 

Bollywood is Bollygood!

❤

"Ravan" ve "Oyuncu Anlatıcılık" Üzerine

Masal anlatmaya yeni başladığım zamanlardı. Kitap kulübümüzde Kurtlarla Koşan Kadınları okuyorduk ve ben de o zaman "La Loba"yı anlatacaktım. Daha sonra defalarca anlatacağım ve hayatımda çok özel bir yeri olan o masalı. Yılların getirmiş olduğu alışkanlıkla masalı ezberlemeye çalıştım ama o kadar olmadı ki... Anlatmaya çalıştım, anlatamadım. Aklımda sürekli kelimeler, bir yapmacık haller. Masaldaki cümleler benim değildi ve bu bana daha önce hiç olmadığı kadar kötü gelmişti. Sonrasında aklımda kalanları yazdım ve kendi tanımlamalarımı buldum. Aslında ilk anlatışımda onların da bir kısmı ezberimdeydi. O gün sezgisel olarak, masal çalışmanın bir oyun çalışmaktan daha farklı olduğunu anladım. O zamanlar, izlenimlerim ve deneyimlerim oyunculuk ve masal anlatıcılığının tamamen iki farklı disiplin olduğu yönündeydi. Bu noktada ise, daha çok keyif aldığım kendimi daha iyi ifade ettiğimi düşündüğüm için "oyunculuktan" tamamen uzaklaşmaya ve salt bir anlatıcı olarak varolmaya çalıştım. Ya da ben öyle olduğunu zannettim çünkü neyi keskin sınırlarla ayırabiliriz ki? Aldığım eğitimlerde anladığım şey, anlatıcının oynamayacağı idi. Evet anlatıcı oynamıyordu ama başka türlü oynamıyordu. Masal anlatımlarını dinledikçe, izledikçe anlatıcıların farklı bir biçimde oynadıklarını gördüm. Bir çok durum, duygu, karakter, otantik kimlikleri ve anlatıcı kimlikleri arasında gidip geldiklerini. Tabi ben bunları kendimde sezemiyordum, bir çok kişi bana oyunculuk eğitiminin masal anlatımında çok işime yaramış olabileceğini söyledi ama ben dumanı üstünde bir masalcı olarak bunlara "hayır ben oyuncu kimliğimden sıyrılmaya çalışıyorum" dedim. Ne cahillik. Aslında bu durum o zamanlar işime yaradı, böylece kendimi yeni bir deneyime açmış oldum. Bildiğim, ezberden yaptığım bir çok şeyden sıyrılıp yeni bir öğrenme sürecine girdim. Deneyimlerimi eskiye dayandırmadan, en baştan. Hiç seyirci karşısına çıkmamış gibi. Aslında bir yandan da bu doğruydu çünkü hiç Sıla olarak seyirci karşısına çıkmamıştım. Aramızda rolden bir duvar vardı. Ama nereden bilecektim ki o rolden duvarın kalınlığı da geçirgenliği de sana bağlı. Böylece anlatıcılık deneyimim başladı ve seyirci, mekan, müzik, masal ilişkisi hakkında bir çok şey öğrendim. Çok farklı deneyimler yaşadım.

2016 yazında sevgili hocam Gürol Tonbul,  Yavuz Ekinci'nin "Günün Birinde" romanında geçen bir masalı uyarladı. Bu masalı Yavuz Ekinci kaleme almıştı. Gürol Hocamla çalışacaktık ve ben anlatacak ama bir yandan da oynayacaktım. Soner Akçay'da bu anlatımda Celo rolünde olacaktı ve İsmail Başışık da müzik yapacaktı, vokal olarak. Aslında projeye başladığımız zamanlarda bende bir çok sinyal yanıp söndü. Nasıl olacaktı? Anlatıcı oynamazdı. Peki buna ne diyecektik? Oyun mu? Anlatım mı? Tiyatro mu? Bu noktada sevgili Gürol hocama sonsuz güvenimi belirtmeliyim. Gürol Hocam çalışmamızın başından beri beni anlatım noktalarında özgür bıraktı ve masal yolculuğunda elimden tuttu. Sonerle, İsmaille olan doğaçlama çalışmalarımızda bize harika kapılar açtı. Çalışmanın başında o anki durumumla anlayamadığım bir çok şey için hocama güvendim ve bir yola çıktık. Uzun sohbetlerimiz oldu. Masal üzerine, anlatıcılık üzerine, hayat üzerine. Bende bir çok noktada ışıkların yanmasının sebebi o sohbetlerdir. Gürol hocam, bu performansta anlatıcının üçlü doğasından bahsetti. Sıla olarak ben, masal anlatıcısı olarak Sıla ve Samiralı Sara olarak masal anlatıcısı.Sonrasında provalara başladığımızda üç farklı hali keşfetmeye başladım. Oyuncu olarak da anlatıcı olarak da yaptığımız şey, bedenimizi ve sesimizi aracı olarak kullanmak. O kişiyi, duyguyu, durumu bedenimize davet etmek. Bunun için özgür bir zihin gerekiyor. Bir oyunda bir karakteri canlandırıyorsam önce onu tanımam, anlamam gerekiyor ve yaptığım şey onun bedenime gelmesine ve benim aracılığımla hikayesini anlatmasına izin vermek. Anlatıcıysam yaptığım şey bir atın, ağacın, rüzgarlı havanın, bir elmanın, bir prensesin bedenim ve sesim aracılığı ile kendini anlatmasına fırsat vermek. Aradan çekilmek ve dahil olmak. Kendimi "oyuncu" ya da "anlatıcı" olarak etiketlememin en büyük nedeni yanlış bir tiyatro anlayışı olduğunu farkediyorum. Beni sınırlayan şey bu olmuş. Kötü örnekler. Yapmacıklı haller, sahte gülüşler. Plastik bir tiyatro anlayışı. Halbuki durumun özü bu değil. Özde, yaptığımız her şeyde bir hikaye anlatıyoruz ve kendimizi aracı kılıyoruz. Ravan'da bunu yapmamış olsaydım nasıl bir şey olduğu hakkında bir fikre sahip olamayacaktım. Bu yüzden Ravan benim için apayrı bir deneyim oldu. Sahne üstünde, yerde ceviz kabukları, bir kilin üstünde ve gölge figürlerle bir dünya yarattık. Yaptığımız şeyin tümü anlatıydı. Her şey o anda oldu. Birbirimizin gözlerinin içine bakıp, enerjimizi hissedip bir masal yarattık. Bir seçim yapmak gerekiyorsa, ben kimim diye, tümü olmayı seçiyorum. Hayatta yaşadığımız her deneyim bizi biz yapıyor. Tüm bu oyuncu anlatıcılık sürecinde öğrendiğim şey bu oldu. Yaşadıklarımı keskin çizgilerle ayıramam, deneyimlerimi alır yoluma devam ederim. Bir bütün olarak.

As the year turns on its axis once again all I can think about at the moment is please, please, please let the ceasefire in Syria hold. What the Syrian people and all refugees have had to endure over the past few years is beyond shameful, and the fighting needs to STOP. We are all part of the same human family, are we not? Stop the fighting, the killing, the detonating of bombs, the helplessness, the despair. Let these be our watchwords for the year ahead:

Help, Share, Give, Enable, Communicate, Understand.

We can all do our bit, and to that end I'm going to invite my friends to join me in what I believe will be a fun way to raise money for charitable causes. 

I'm calling it the £20 Challenge.

We will all start with a single £20 note, and using that money will, over the course of one year, try and generate as much money as we can using our creative skills and ingenuity, and pledge that at the year's end we will donate whatever sum we have managed to raise to a charity of our choosing. It can become a bit of a competition between friends if you like. Would you like to take part in the £20 Challenge too?

That initial £20 could be engaged in the simple buying and selling on of an object, or if you are creative £20 could buy some fabric and some buttons and some pads to make cushion covers, and they could be sold to make a profit. If you are good at baking, then some of the £20 could buy the ingredients to bake a cake or scones to sell at a produce market; or invite family/friends round for a meal but ask guests to pay for their food; the equivalent of what it would have cost them to eat out at a restaurant or pub. Or make greetings cards and sell them to your friends; the possibilities are endless! As your pot of money grows you will have more funds to invest in money-making ideas. Sometimes you may not make much of a profit, but it will all contribute to the growing fund. It will involve keeping an accurate record of exactly what you buy and sell, and how much money you have made as you go along. I just wonder how much can actually be generated from one £20 note in the course of a year......

So, are you up for the challenge?
I will post regularly through the year on how we progress with the challenge, and I would love it if you shared your experience too.
I wish you all a very Happy New Year!
xxx

Masal ve Hikaye Kitaplarım

Geçtiğimiz günlerde İnstagram'da Kumkurdu kitabından bir bölüm paylaşmıştım. O paylaşımımdan sonra bir kaç arkadaşım Asya Mavi'ye okuduğum kitapları ve kendi masal kitaplarımı merak ettiklerini söylediler. Ben de üşenmedim kitaplığımdan en sevdiklerimi topladım kucağıma yatağa yığdım. Şimdi de onları teker teker yazacağım. Kendi okuduğum masal kitaplarının büyük kısmını kütüphaneden temin ediyorum. Mitoloji ve masal kitapları oluyor onlar ancak iade ettiğim için isimlerini şimdi sizlerle paylaşamayacağım. Bu paylaştıklarım benim kitaplığımda olup da özellikle çok sevdiklerim. Sizin de sevdiğiniz masal kitapları varsa yorum kısmına eklerseniz çok sevinirim. Burada güzel bir paylaşım başlatmış oluruz. Hepimize keyifli okumalarla geçen güzel bir yıl olsun.

Benim Masal Kitaplarım

1) Hortlağın 25 Öyküsü - İmge Kitabevi
2)En Güzel Macar Masalları - Nesin Yayınevi
3)Efsunlu Hayvan Masalları - İtalo Calvino - YKY
4)Büyülü Kuş - İtalo Calvino - YKY
5)Türk Masalları - Naki Tezel - T.C. Kültür Bakanlığı
6)Dilenci Kral ve Mutluluğun Sırrı - Joel Ben Izzy - Koridor
7)Rus Yazarlardan Masallar ve Şiirler - YKY
8)Ermeni Masalları - Pencere Yayınları
9)Zaman Zaman İçinde- Pertev Naili Boratav - RK


Asya Mavi'nin Hikaye Kitapları

1) Kumkurdu - Asa Lind - Pegasus
2)Daha Fazla Kumkurdu - Asa Lind - Pegasus
3) Daha  Da Fazla Kumkurdu- Asa Lind - Pegasus
4) Sakar Cadı Vini'nin Dinazoru - Valerie Thomas ve Korkly Paul - Türkiye İş Bankası Yayınları
5)Sakar Cadı Vini Uzayda - Valerie Thomas ve Korkly Paul - Türkiye İş Bankası Yayınları
6)Sakar Cadı Vini'nin Kış Macerası - Valerie Thomas ve Korkly Paul - Türkiye İş Bankası Yayınları
7)Sakar Cadı Vini'nin Doğumgünü - Valerie Thomas ve Korkly Paul - Türkiye İş Bankası Yayınları
8)Frederick - Leo Lionni - Elma Çocuk
9)Binbir Oyun - Henri Tullet - Timaş
10)Şuşu ve Üçtekeri - Yıldıray Karakiya, Başak Günaçan - Redhouse Kidz
11)Şuşu, Can ve Dörtteker-  Yıldıray Karakiya, Başak Günaçan - Redhouse Kidz
12)Gergedanlar Krep Yemez - Anna Kemp & Sara Ogilvie - Pearson
13) Başka Bir Anne - Sandra Albulrek , Sebban Leyla Navaro- Can Çocuk
14)Masal Battaniyesi - Ferida Wolff, Harriet May Savitz - Nesin Yayınevi
15)Koş Balkabağım Koş - Eva Mejuto , Andre Letria - Redhouse Kidz
16)Bütün Gün Esneyen Prenses - Carmen Gil, Elena Odrizola - Redhouse Kidz
17)Kütüphanedeki Aslan - Michelle Knudsen - Tudem
18)Mutlu Suaygırı - Richard Edwards ve Carol Liddiment - Türkiye İş Bankası Yayınları
19)Picasso ve At Kuyruğu Saçlı Kız - Laurence Anholt - Pearson

Post-truth science?

This year was one that shook normal politics to its core.  Our belief in free and fair elections, in the idea that politicians strive to tell the truth and are ashamed to be caught lying, in real news vs fake, in the importance of tradition and precedent, indeed in the importance of science in shaping our world, have all been challenged.  This has served to remind us that we can't take progress, world view, or even truth and the importance of truth themselves for granted.  The world is changing, like it or not.  And, as scientists who assume that truth actually exists and whose lives are devoted to searching for it, the changes are not in familiar directions.  We can disagree with our neighbors about many things, but when we can't even agree on what's true, this is not the 'normal' world we know.

To great fanfare, Oxford Dictionaries chose "post-truth" as its international word of the year.

The use of “post-truth” — defined as “relating to or denoting circumstances in which objective facts are less influential in shaping public opinion than appeals to emotion and personal belief” — increased by 2,000 percent over last year, according to analysis of the Oxford English Corpus, which collects roughly 150 million words of spoken and written English from various sources each month.  New York Times

I introduce this into a science blog because, well, I see some parallels with science.  As most of us know, Thomas Kuhn, in his iconic book, The Structure of Scientific Revolutions, wrote about "normal science", how scientists go about their work on a daily basis, theorizing, experimenting, and synthesizing based on a paradigm, a world view that is agreed upon by the majority of scientists.  (Although not well recognized, Kuhn was preceded in this by Ludwik Fleck, Polish and Israeli physician and biologist who, way back in the 1930s, used the term 'thought collective' for the same basic idea.)

When thoughtful observers recognize that an unwieldy number of facts no longer fit the prevailing paradigm, and develop a new synthesis of current knowledge, a 'scientific revolution' occurs and matures into a new normal science.  In the 5th post in Ken's recent thought-provoking series on genetics as metaphysics, he reminded us of some major 'paradigm shifts' in the history of science -- plate tectonics, relativity and the theory of evolution itself.

We have learned a lot in the last century, but there are 'facts' that don't fit into the prevailing gene-centered, enumerative, reductive approach to understanding prediction and causation, our current paradigm.  If you've read the MT for a while, you know that this is an idea we've often kicked around.  In 2013 Ken made a list of 'strange facts' in a post he called "Are we there yet or do strange things about life require new thinking?" I repost that list below because I think it's worth considering again the kinds of facts that should challenge our current paradigm.

As scientists, our world view is supposed to be based on truth.  We know that climate change is happening, that it's automation not immigration that's threatening jobs in the US, that fossil fuels are in many places now more costly than wind or solar.  But by and large, we know these things not because we personally do research into them all -- we can't -- but because we believe the scientists who do carry out the research and who tell us what they find.  In that sense, our world views are faith-based.  Scientists are human, and have vested interests and personal world views, and seek credit, and so on, but generally they are trustworthy about reporting facts and the nature of actual evidence, even if they advocate their preferred interpretation of the facts, and even if scientists, like anyone else, do their best to support their views and even their biases.

Closer to home, as geneticists, our world view is also faith-based in that we interpret our observations based on a theory or paradigm that we can't possibly test every time we invoke it, but that we simply accept.  The current 'normal' biology is couched in the evolutionary paradigm often based on ideas of strongly specific natural selection, and genetics in the primacy of the gene.

The US Congress just passed a massive bill in support of normal science, the "21st Century Cures Act", with funding for the blatant marketing ploys of the brain connectome project, the push for "Precision Medicine" (first "Personalized Medicine, this endeavor has been, rebranded -- cynically? --yet again to "All of Us") and the new war on cancer.  These projects are nothing if not born of our current paradigm in the life sciences; reductive enumeration of causation and the ability to predict disease.  But the many well-known challenges to this paradigm lead us to predict that, like the Human Genome Project which among other things was supposed to lead to the cure of all disease by 2020, these endeavors can't fulfill their promise.

To a great if not even fundamental extent, this branding is about securing societal resources, for projects too big and costly to kill, in a way similar to any advertising or even to the way churches promise heaven when they pass the plate. But it relies on wide-spread acceptance of contemporary 'normal science', despite the unwieldy number of well-known, misfitting facts.  Even science is now perilously close to 'post-truth' science. This sort of dissembling is deeply built into our culture at present.

We've got brilliant scientists doing excellent work, turning out interesting results every day, and brilliant science journalists who describe and publicize their new findings. But it's almost all done within, and accepting, the working paradigm. Too few scientists, and even fewer writers who communicate their science, are challenging that paradigm and pushing our understanding forward. Scientists, insecure and scrambling not just for insight but for their very jobs, are pressed explicitly or implicitly to toe the current party line. In a very real sense, we're becoming more dedicated to faith-based science than we are to truth.

Neither Ken nor I are certain that a new paradigm is necessary, or that it's right around the corner. How could we know? But, there are enough 'strange facts', that don't fit the current paradigm centered around genes as discrete, independent causal units, that we think it's worth thinking about whether a new synthesis, that can incorporate these facts, might be necessary. It's possible, as we've often said, that we already know everything we need to know: that biology is complex, genetics is interactive not iterative, every genome is unique and interacts with unique individual histories of exposures to environmental risk factors, evolution generates difference rather than replicability, and we will never be able to predict complex disease 'precisely'.

But it's also possible that there are new ways to think about what we know, beyond statistics and population-based observations, to better understand causation.  There are many facts that don't fit the current paradigm, and more smart scientists should be thinking about this as they carry on with their normal science.



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Do strange things about life require new concepts?

1.  The linear view of genetic causation (cis effects of gene function, for the cognoscenti) is clearly inaccurate.  Gene regulation and usage are largely, if not mainly, not just local to a given chromosome region (they are trans);

2.  Chromosomal usage is 4-dimensional within the nucleus, not even 3-dimensional, because arrangements are changing with circumstances, that is, with time;

3.  There is a large amount of inter-genic and inter-chromosomal communication leading to selective expression and non-expression at individual locations and across the genome (e.g., monoallelic expression).  Thousands of local areas of chromosomes wrap and unwrap dynamically depending on species, cell type,  environmental conditions, and the state of other parts of the genome at a given time; 

4.  There is all sorts of post-transcription modification (e.g., RNA editing, chaperoning) that is a further part of 4-D causation;

5.  There is environmental feedback in terms of gene usage, some of which is inherited (epigenetic marking) that can be inherited and borders on being 'lamarckian';

6.  There are dynamic symbioses as a fundamental and pervasive rather than just incidental and occasional part of life (e.g., microbes in humans);

7.  There is no such thing as 'the' human genome from which deviations are measured.  Likewise, there is no evolution of 'the' human and chimpanzee genome from 'the' genome of a common ancestor.  Instead, perhaps conceptually like event cones in physics, where the speed of light constrains what has happened or can happen, there are descent cones of genomic variation descending from individual sequences--time-dependent spreading of variation, with time-dependent limitations.  They intertwine among individuals though each individual's is unique.  There is a past cone leading of ancestry to each current instance of a genome sequence, from an ever-widening set of ancestors (as one goes back in time) and a future cone of descendants and their variation that's affected by mutations.  There are descent cones in the genomes among organisms, and among organisms in a species, and between species. This is of course just a heuristic, not an attempt at a literal simile or to steal ideas from physics! 

Light cone: Wikipedia

8.  Descent cones exist among the cells and tissues within each organism, because of somatic mutation, but the metaphor breaks down because they have strange singular rather than complex ancestry because in individuals the go back to a point, a single fertilized egg, and of individuals to life's Big Bang;

9.  For the previous reasons, all genomes represent 'point' variations (instances) around a non-existent core  that we conceptually refer to as 'species' or 'organs', etc.('the' human genome, 'the' giraffe, etc.);

10.  Enumerating causation by statistical sampling methods is often impossible (literally) because rare variants don't have enough copies to generate 'significance', significance criteria are subjective, and/or because many variants have effects too small to generate significance;

11.  Natural selection, that generates current variation along with chance (drift) is usually so weak that it cannot be demonstrated, often in principle, for similar statistical reasons:  if cause of a trait is too weak to show, cause of fitness is too weak to show; there is not just one way to be 'adapted'.

12.  Alleles and genotypes have effects that are inherently relativistic.  They depend upon context, and each organism's context is different;

13.  Perhaps analogously with the ideal gas law and its like, phenotypes seem to have coherence.  We each have a height or blood pressure, despite all the variation noted above.  In populations of people, or organs, we find ordinary (e.g., 'bell-shaped') distributions, that may be the result of a 'law' of large numbers: just as human genomes are variation around a 'platonic' core, so blood pressure is the net result of individual action of many cells.  And biological traits are typically always changing;

14. 'Environment' (itself a vague catch-all term) has very unclear effects on traits.  Genomic-based risks are retrospectively assessed but future environments cannot, in principle, be known, so that genomic-based prediction is an illusion of unclear precision; 

15.  The typical picture is of many-to-many genomic (and other) causation for which many causes can lead to the same result (polygenic equivalence), and many results can be due to the same cause (pleiotropy);

16. Our reductionist models, even those that deal with networks, badly under-include interactions and complementarity.  We are prisoners of single-cause thinking, which is only reinforced by strongly adaptationist Darwinism that, to this day, makes us think deterministically and in terms of competition, even though life is manifestly a phenomenon of molecular cooperation (interaction).  We have no theory for the form of these interactions (simple multiplicative? geometric?).

17.  In a sense all molecular reactions are about entropy, energy, and interaction among different molecules or whatever.  But while ordinary nonliving molecular reactions converge on some result, life is generally about increasing difference, because life is an evolutionary phenomenon.

18. DNA is itself a quasi-random, inert sequence. Its properties come entirely from spatial, temporal, combinatorial ('Boolean'-like) relationships. This context works only because of what else is in (and on the immediate outside) of the cell at the given time, a regress back to the origin of life.

Is genetics still metaphysical? Part VI. What might lead to a transformative insight in biology today--if we need one

It's easy to complain about the state of the world, in this case, of the life sciences, and much harder to provide the Big New Insights one argues might be due.  Senioritis makes it even easier: when my career in genetics began, not very much was known.  Genes figuratively had 2 alleles, with measurable rates of recurrence by mutation.  Genetically tractable traits were caused by the proteins in these genes; quantitative traits were too complex to be considered seriously to be due to individual genes, so were tacitly assumed to be the additive result of an essentially infinite number of them.

How many genes there were was essentially unknowable, but using identified proteins as a gauge, widely thought to be around 100,000. The 'modern evolutionary synthesis' solved the problem, conceptually, by treating these largely metaphorical causal items as largely equivalent, if distinct, entities whose identities were essentially unknowable.  That is, at least, we didn't have to think about them as specific entities, only their collective actions.  Mendelian causal genes, evolving by natural selection was, even if metaphorical or even in a serious way metaphysical, a highly viable worldview in which to operate.  A whole science enterprise grew around this worldview.  But things have changed.

Over the course of my career, we've learned a lot about these metaphysical units.  Whether or not they are now more physical than metaphysical is the question I've tried to address in this series of posts, and I think there's not an easy answer--but what we have, or should have, understood is that they are not units!  If we have to have a word for them, perhaps it should be interactants.  But even that is misleading because the referents are not in fact unitary.  For example, many if not  most 'genes' are only active in context-dependent circumstances, are multiply spliced, may be post-trascriptionally edited, are chemically modified, and have function only when combined with other units (e.g., don't code for discretely functioning proteins), etc.

Because interaction is largely a trans phenomenon--between factors here and there, rather than just everything here, the current gene concept, and the panselectionistic view in which every trait has an adaptive purpose, whether tacit or explicit, is a serious or even fundamental impediment to a more synthetic understanding. I feel it's worth piling on at this point, and adding that the current science is also pan-statistical in ways that in my view are just as damaging.  The reason, to me, is that these methods are almost entirely generic, based on internal comparison among samples, using subjective decision-criteria (e.g., p-values) rather than testing data against a serious-level theory.

If this be so, then perhaps if the gene-centered view of life, or even the gene concept itself as life's fundamental 'atomic' unit, needs to be abandoned as a crude if once important approximation to the nature of life. I have no brilliant ideas, but will try here to present the sorts of known facts that might stimulate some original thinker's synthesizing insight--or, alternatively, might lead us to believe that no such thing is even needed, because we already understand the relevant nature of life: that as an evolutionary product it is inherently not 'regular' the way physics and chemistry are.  But if our understanding is already correct, then our public promises of precision medicine are culpably misleading slogans.

In part V of this series I mentioned several examples of deep science insight, that seemed to have shared at least one thing in common:  they were based on a synthesis that unified many seemingly disparate facts.  We have many facts confronting us.  How would or might we try to think differently about them?  One way might be to ask the following questions: What if biological causation is about difference, not replication?  What if 'the gene' is misleading, and we were to view life in terms of interactions rather than genes-as-things?  How would that change our view?

Here are some well-established facts that might be relevant to a new, synthetic rather than particulate view of life:

1. Evolution works by difference, not replication Since Newton or perhaps back to the Greek geometers, what we now call 'science' largely was about understanding the regularities of existence.  What became known as 'laws' of Nature were, initially for theological reasons, assumed to be the basis of existence.  The same conditions led to the same outcomes anywhere.  Two colliding billiard balls here on Earth or in any other galaxy, would react in identical ways (yes, I know, that one can never have exactly the same conditions--or billiard balls--but the idea is that the parts of the cosmos were exchangeable.)  But one aspect of life is that it is an evolved chemical phenomenon whose evolution occurred because elements were different rather than exchangeable.  Evolution and hence life, is about interactions or context-specific relative effects (e.g., genetic drift, natural selection). 

2.  Life is a phenomenon of nested (cladistic) tree-like relationships Life is not about separated, independent entities, but about entities that from the biosphere down (at least) to individual organisms are made of sets of variations of higher-level components.  Observation at one level, at least from cells up to organs to systems to individuals, populations, species and ecosystems, are reflections of the nested level(s) the observational level contains. 

3.  Much genetic variation works before birth or on a population level Change may arise by genetic mutation, but function is about interactions, and success--which in life means reproduction--depends on the nature of the interactions at all levels.  That is, Darwinian competition among individuals of different species is only one, and perhaps one of the weakest, kinds of such interaction.  Embryonic development is a much more direct, and stronger arena for filtering interactions, than competition (natural selection) among adults for limited resources.  In a similar way, some biological and even genetic factors work only in a population way (bees and ants are an obvious instance, as are bacterial microfilm and the life cycles of sponges or slime molds). 

4.  Homeostasis is one of the fundamental and essential ways that organisms interact Homeostasis as an obvious example of a trans phenomenon.  It's complexly trans because not only do gene-expression combinations change, but they are induced to change by extra-cellular and even extra-organismal factors both intra and inter-species.  The idea of a balance or stasis, as with organized and orchestrated combinatorial reaction surely cannot be read of in cis.  We have known about interactions and reactions and so on, so this is not to invoke some vague Gaia notions, but to point out the deep level of interactions, and these depend on many factors that themselves vary, etc. 

5. Environments include non-living factors as well as social/interaction ones No gene is an island, even if we could identify what a 'gene' was, and indeed that no gene stands alone is partly why we can't.  Environments are like the celestial spheres: from each point of view everything else is the 'environment', including the rest of a cell, organ, system, organism, population, ecosystem.  In humans and many other species, we must include behavioral or social kinds of interactions as 'environment'.  There is no absolute reference frame in life any more than in the cosmos.  Things may appear linear from one point of view, but not another.  The 'causal' effects of a protein code (a classical 'gene') depend on its context--and vice versa. 

6. The complexity of factors often implies weak or equivalent causation--and that's evolutionarily fundamental. Factors or 'forces' that are too strong on their own--that is, that appear as individually identifiable 'units'--are often lethal to evolutionary survival.  Most outcomes we (or evolution) care about are causally complex, and they are always simultaneously multiple: a species isn't adapting to just one selective factor at a time, for example.  Polygenic causation (using the term loosely to refer to complex multi-factoral causation) is the rule.  These facts mean that individually identified factors usually have weak effects and/or that there are alternative ways to achieve the same end, within or among individuals.  Selection, even of the classical kind, must be typically weak relative to any given involved factor. 

7. The definition of traits is often subjective and affects their 'cause' Who decides what 'obesity', 'intelligence', or 'diabetes' is?  In general, we might say that 'Nature' decides what is a 'trait', but in practice it is often we, via our language and our scientific framework, who try to divide up the living world into discrete categories and hence to search for discrete causal factors.  It is no surprise that what we find is rather arbitrary, and gives the impression of biological causation as packaged into separate items rather than being fundamentally about a 'fabric' of interactions.  But the shoehorn is often a major instrument in our causal explanations. 

8. The 'quantum mechanics' effect: interaction affects the interactors In many aspects of life, obviously but not exclusively applied to humans, when scientists ask a question or publicize a result, it affects the population in question.  This is much like the measurement effect in quantum mechanics.  Studying something affects it in ways relevant to the causal landscape we are studying.  Even in non-human life, the 'studying' of rabbits by foxes, or of forests by sunlight, affects what is being studied.  This is another way of pointing out the pervasive centrality of interaction.  Just like political polls, the science 'news' in our media, affect our behavior and it is almost impossible to measure the breadth and impact of this phenomenon.

All of these phenomena can be shoe-horned into the 'gene' concept or a gene-centered view of life or of biomedical 'precision'.  But it's forced: each case has to be treated differently, by statistical tests rather than a rigorous theory, and with all sorts of exceptions, involving things like those listed here, that have to be given post hoc explanations (if any). In this sense, the gene concept is outmoded and an overly particulate and atomized view of a phenomenon--life--whose basic nature is that it is not so particularized.

Take all of these facts, and many others like them, and try to view them as a whole, and as a whole that, nonetheless can evolve.  Yesterday's post on how I make doggerel was intended to suggest a similar kind of mental exercise.  There can be wholes, and they can evolve, but they do it as wholes. If there is a new synthesis to be found, my own hunch it would be in these sorts of thoughts.  As with the examples I discussed a few days ago (plate techtonics, evolution itself, and relativity), there was a wealth of facts that were not secret or special, and were well-known. But they hadn't been put together until someone thinking hard about them, who was also smart and lucky, managed it. Whether we have this in the offing for biology, or whether we even need it, is what I've tried to write about in this series of posts.

Of course, one shouldn't romanticize scientific 'revolutions'.  As I've also tried to say, these sorts of facts, which are ones I happen to have thought of to list, do not in any way prove that there is a grand new synthesis out there waiting to be discovered. It is perfectly plausible that this kind of ad hoc, chaotic view of life is what life is like.  But if that's the case, we should shed the particulate, gene-centered view we have and openly acknowledge the ad hoc, complex, fundamentally trans nature of life--and, therefore, of what we can promise in terms of health miracles.