reviewing for my Genes final

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I'm reviewing for my Genes and the Human Condition final.

Here are three quotes from the lectures:


The satirist Jonathan Swift told us that it was not possible to reason someone out of a position that they didn’t reason themselves into.  

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Around the world, more than 170 million hectares of land are under engineered crops, sustained by 16 million farmers in 28 countries, with no reports of apparent damage to health or the environment.

"...no reports of apparent damage to health or the environment."  NO reports.  That's a pretty strong statement.......

Another quote:

In fact, as the European Commission itself found in a 2010 survey of hundreds of scientific studies, there is simply no evidence that transgenic crops put the health of humans or the environment at increased risk. Overwhelmingly other independent surveys show the same thing.


I know that humanity has nearly always been gung-ho to do whatever seems to serve our short-term interests, without regard for what will happen next.  (Hence the disappearance of passenger pigeons -- once "the most common bird on the planet," with flocks in the billions -- we killed them all, every last one.....)

I also know that I should take into account what a speaker's bias is, when I listen.  I know that my genetics professors are working on transgenic projects in their own labs (one is working on a fungus which will kill malaria-carrying mosquitoes AND the malaria-causing protozoan they carry!).  Their bias is that biotechnology is the way of the future, opening doors for amazing progress on many, many fronts.

The benefits they dangle are tantalyzing -- better treatments for cancer, vastly lessened use of pesticides, the possibility of fixing (not treating, FIXing) some genetic diseases, increased crop yields (c4 photosynthesis rather than c3, for one change), and -- bringing back species we exterminated, like passenger pigeons.  Just to name a few.....

Looking at history, I am sure there will also be unexpected negative consequences (and some of those will be disasters)..........................

And yet.  The potential benefits from many of these areas of study are so big it's hard to get my mind around them.

Currently we spread an unconscionable amount of poison everywhere, all the time.  Insecticides, fungisides, you name it -- if we don't like it, we poison it.  Even though we are clear, now, that there are enormous long-term consequences.  If we enable plants to better resist predators, in ways that are much more closely targeted to their particular predators, we could lessen our use of pesticides -- which we KNOW are harmful to us and to the planet.

Chemotherapy poisons everything it touches, with the hope that the disease will be killed while the patient lives.  A much more focused approach makes more sense.  Both because it is more likely to kill the cancer's rogue cells, and because it will be less harmful to the body's normal cells.


I'm not thinking that slamming the door on biotechnology is the right thing to do............................

Another truth is that a lot of these changes are meant to benefit the most needy.  Stopping malaria, for example.  Or -- what about Golden Rice?  Golden Rice, a transgenic plant, has significant amounts of vitamin A (hence the golden grains of rice for which it is named).  It grows in places where large numbers of people suffer from vitamin A deficiency (which causes blindness, for one thing, and hampers children's immune systems, for another). 

People in the developed world, who have access to all the vitamin A they want, are preventing use of Golden Rice by people who desperately need that vitamin A.

We trashed the world, any old way we pleased, getting to our "developed" status.

It seems to me it is pretty darn hypocritical of us to deny others the benefits of technology, because "something bad might happen".............  (Especially when we are still strip mining, and fracking, and spreading pesticides which have been banned in other places.........)

It is in my nature to look for all of the bad things that might result from a change.

But I am thinking that the benefits of our current biotechnological direction(s) are so vast that we need to be really careful to listen to the science, rather than to emotion, when we make decisions about what are, and are not, good directions to take.

Let us NOT be those people Johnathan Swift was referring to, who are unmoved by reason!

What is the *evidence*?  

If the truth is -- "NO reports of apparent damage to health or the environment," then we need to let that be our guide, rather than letting our fears of what MIGHT happen stop us from doing some amazing things that might even go a long way toward repairing the damage we've done in the past.................

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another TED talk from the "extra info" in Genes class

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Here's a TED talk on de-extinction (bringing back passenger pigeons, for example), which I learned about from the extra info in Genes and the Human Condition.

What we can do, right now, is mind-bending.  SO much more than I knew.

And the knowledge/technology in this area is increasing faster than Moore's Law.........

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Um. Not sure this is a good thing............................

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From the final week of Genes and the Human Condition:

With a lab with cheap equipment (like a $260 centrifuge you can build from a kit), you can clone and sequence a gene in a couple of days using freely downloadable protocols.

Kay Aull built her own genetic testing kit in a small room in Cambridge, Massachusetts.  In her makeshift lab, she analyzed a specific gene mutation lined to a gene her father was diagnosed with, called hemochromatosis.  Kay Aull tested her own DNA, to discover she is a carrier of her father's disease, but unlikely to carry the disease herself.

Genspace in Brooklyn, New York is an example of a state-of-the-art DIY biolaboratory, available to biohackers for $100 a month.

The ideas and the drive behind these people are reminiscent of the early computer pioneers who wrote the software (and developed the hardware) that kickstarted the computer revolution.

 

Hmmmm.

The open "freely available" way a LOT of genetic info and technology are handled means that scientists can make progress a lot faster than when things are secret and tightly controlled.

It also means, it seems to me, that some ***extremely*** powerful tools are in the hands of every random person, and not all of them will have pure hearts and good intentions.........


Yikes.


Here's a link to a TED talk by the founder of Genspace.....  She addresses these concerns.

I try to take into consideration what anyone's motivation is, for trying to sell me something.  Her bias is clearly on the side of making all of this science and technology freely available.  But she's convincing........

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Scientists Just Sequenced DNA From A 400,000-Year-Old Early Human

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Wow. 

In Genes class, we just (a couple of weeks ago) heard that the oldest DNA that has been successfully sequenced is from a (frozen) horse that died 700,000 years ago.

Just now, I learn Scientists Just Sequenced DNA From A 400,000-Year-Old Early Human.  This is much older than any DNA previously sequenced from proto-human remains.....

You can see what  I meant, a couple of days ago, about the data changing practically every day!  As the science allows the technology to improve, we are capable of learning more and more, from older and older bones............

Amazing.


Also interesting is that these 400,000-yr-old bones, found in Spain, are apparently very closely related to Denisovans, previously only known from a few pieces of bone -- in Siberia!!!  It's possible that those people in Spain actually *are* Denisovans, which would give us the first ability to see what they may have looked like.


I'll say again that given how unlikely it is that anything that has lived will become a fossil, and then how unlikely it is that the fossil will be preserved for long periods of time, and then how unlikely it is that we will find that fossil, I'm boggled at how much we know (and are learning, every day) about what happened in the distant past.  !!!

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kindness.....

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One of the topics in Genes and the Human Condition is sexual selection.  Which of the traits that people have preferred in mates have changed us over time?

One that was mentioned is blue eyes.  Apparently one individual, about 8000 years ago, showed up with blue eyes.  This was such a popular characteristic that now hundreds of millions of people have blue eyes.



We were told that researchers asked people all over the planet what they valued in a potential mate.  The top two, everywhere, for women and for men, are intelligence and kindness.  !!!
 
(More or less) as our instructor put it:  you may scoff at the notion of us being kind to each other.  But consider -- you can fill a football stadium with tens of thousands of complete strangers, and we basically tick along just fine.  If you tried to put thousands of our closest relatives -- chimps -- in that sort of close proximity, you would have slaughter.

Hmm.  Everything *is* relative.....  Most of us do encounter hundreds or thousands of strangers, at least from time to time, and mostly everything is fine..............


This may be the most encouraging thing I've encountered in a while, in re human behavior!

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I'm looking through some of the outside resources

for Genes and the Human Condition.

Robert Sapolsky, on the physiological effects of stress:

But many of the qualities that make us human also can induce stress, he noted. "We can be pained or empathetic about somebody in Darfur," he said. "We can be pained by some movie character that something terrible happens to that doesn't even exist. We could be made to feel inadequate by seeing Bill Gates on the news at night, and we've never even been in the same village as him or seen our goats next to his." 


Damn it, Bill Gates!  We've never been in the same village, but I just KNOW your goats are cooler than mine!

lol....................



This is something I've been thinking for a long time. No, I have not been thinking about  Bill Gates, nor even Bill Gate's no doubt excellent goats.  (Well, ok, I do think about Bill Gates, if not his goats, when I struggle, once a year, to print envelopes in which to send holiday letters............................  Bill, if you can hear my thoughts, this is an area that could use some solid improvement.  Every year this takes me too long and is very frustrating!)

Ahem.  Let's get back on track, shall we?



What I've been thinking about, off and on, over time, is this -- it's a truism that our strengths are also our weaknesses.  It's true for us as individuals (at least some of the time under some circumstances).

It's also true for us as a species............

We have the capacity to think about what happened in the past, and to imagine what might happen in the future.  We can use that capacity to attempt to optimize our futures (and sometimes we even do so!).

We can also use it to drive ourselves nuts, keeping ourselves awake at night wondering if that weird noise the dog just made means he ought to be rushed to the vet, or stressing out over something totally stupid like Bill Gates having cooler goats than we'll ever have.........


I like it when a conclusion I've drawn shows up, confirmed, in someone's research!
 

It's an interesting article.

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What makes humans different from other sorts of organisms?

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I've heard a lot, in Genes and the Human Condition, about what makes us the same as others, and what makes us different.

My very favorite graphic, so far, shows a section of DNA as it is found in chickens, in chimps, and in us.  Mostly the same in all of us, but................

I didn't find a copyright-free version of the image to show you.  If you click on this link, and scroll down, you will find a mostly-gray rectangular image in the middle (left/right-wise) that has pics of a man, a chimp, and a chicken.  In a magenta band at the top of the image, it says "Scanning the Genome."  The image shows the sequence of DNA, as it's found in chickens, chimps, and humans.

You may recall my reporting from Dino 101 that there is clear and compelling evidence that chickens (and the rest of the birds) are descended directly from dinosaurs.  You may also recall my post about dimetrodon, which talks about how we know we are more closely related to dimetrodon than we and dimetrodon were related to dinosaurs.

The last common ancestor for chickens (and dinos!) and chimps (and us) was before dimetrodon.  Before synapsids and diapsids went their separate ways.  Long before the first dinos walked the Earth.

In Genes, the estimate for the last common ancestor for chickens and chimps (and us) was 300,000,000 years ago. Chimps and chickens show almost the same DNA sequence, even after 300,000,000 years of separate evolution.  (Which is kind of amazing in itself, don't you think?)  Dinos, from whom chickens have inherited this DNA, presumably had the same sequence we see in chickens today. 

(Digression -- If I understand correctly what Ive been taught -- when a section of DNA is as similar as this between two organisms that haven't had a common ancestor in 300,000,000 years, we believe the DNA is unchanged over that amount of time.  This indicates DNA that is essential to an organism -- most changes to this DNA are fatal.  End of Digression.)

Katharine Pollard and her team look for the areas of the human genome that differ the most from the chimp genome.  H(uman) A(ccelerated) R(egion) is the name Pollard et al have given to sections of DNA that are the most different between us and chimps.  The HARs are numbered by the degree of difference.

The section of DNA in the graphic is HAR1.  It is the section of our genome that shows the most difference from the corresponding section in the chimp genome.  HAR1 is about brain development.

Notice that the difference in this sequence, between chimps and chickens after 300,000,000 years of separate evolution is only two changes.

Current thinking is that we and chimps had our last common ancestor 7-7.5 million years ago.  In that relatively short span of time, our version of the HAR1 section of DNA has changed by 18 differences from the chimp version of this section of DNA.

(Digression -- Don't you think this was a smart way to look for the things that make us the most different from chimps?  (Note also the illustrations that follow the one I'm talking about -- HAR2 is about development of wrists and thumbs........  End of digression.)



My very favorite thing about the graphic is that they chose a descendant of dinos to include.  (For all I know, they could have included a turtle.  Or a fruit fly.....  But they picked a dino's child.............)

I am tickled to have that chicken (and her dino ancestry!) included in the info about genetic change over time.

I love it when what I learn in one place connects to and enriches what I learned somewhere else.........

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immersed in genetics

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I am immersed in genetics.  In Plants class we got a taste of epigenetics -- the heritable (!!!) influence of environment on gene expression.  There's a Coursera class on epigenetics, but it needs a "basic genetics" class as a prerequisite, so I'm taking one now.  I started it when it was already 2 weeks into a 6-week class.  I was still in Plants and Dinos at that point, so I didn't start paying attention to Genetics until the last several days. 

I discovered this weekend that I could still pass Genetics if I buckled right down to it, so that's what I'm doing.  As of about half an hour ago, I have listened to all of the lectures, and have taken all the quizzes, for weeks 1-4 of the class.  I still need to take the midterm (on weeks 1-3), and then I'll be caught up.  Week 5 starts tomorrow..........

Genes and the Human Condition is really interesting!!!  Especially as what we know about genetics and epigenetics keeps updating every 5 minutes, in large part because the computer technology that lets us sequence (and compare) genomes gets better every minute.....  (Something of an exaggeration, but not much!)

The things we are learning in this class -- about ourselves compared to other living organisms, and about ourselves compared to Neanderthals and other extinct forms of humans..............  Mind-bending.

One random human varies from an unrelated other human, on average, about one in every thousand base pairs (a "base pair" is one rung on a DNA ladder).  The human genome varies from the chimp genome by about one in every hundred base pairs.  That means we are only ten times more different from chimps than any one of us is different from other people we're not related to.  !!!

Mind-bending!

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my newest class..........

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Genes and the Human Condition (From Behavior to Biotechnology) is my latest venture into Coursera's offerings.

I thought the glimpse of epigenetics that we got in What a Plant Knows was really interesting.  One of my Plants classmates said Coursera has a class on epigenetics, so I went to check it out.  The epigenetics prof said we'd better have a foundation in basic genetics, and listed a bunch of classes that could give us that foundation.

My first thought was -- "I know about basic genetics."  My second thought was -- "Yeah, well, you thought you'd remember algebra, too........."

Um.  Yes. 

Hmmm.

I took a look at the list of recommended genetics classes.  Genes and the Human Condition is six weeks long.  I joined it two weeks into the course, when I was still in Plants and Dinos.  Only this week have I been seriously listening to Genes (starting when the class was half over).

It is really dense!  Many lectures, all densely packed with (fascinating) content.  So far, I am really impressed.  They are doing a very good job of presenting the content, with lots of interesting examples and great analogies ("Your personal genome is like two cookbooks -- one from your mother, and one from your father.  You may get two identical recipes for a  particular dish, or you may get two different recipes."  And clips holding bunches of pages shut, standing in for tightly folded DNA that isn't being expressed....  Excellent visual!).


I'm not expecting to "pass" this class (by doing all the work up to whatever standard they are setting) as I have joined the class so late.  I do expect to listen to all the lectures (perhaps more than once!).  I don't know if I'll learn enough to be able to keep my head above water in the epigenetics class, but that's ok -- I'm learning a lot of very interesting stuff!

This morning I listened to a lecture about genomics.  When he talked about comparing one genome to another (human to chimp, say), he said we may care more about what is different than about what is the same.  We and chimps are exceedingly closely related.  Chimps are more closely related to us than they are to gorillas......

Here's something he talked about that was completely new to me.

That's an adult human skull on the left, and an adult chimp's skull on the right.  Whose skull is in the middle?

That's a baby chimp's skull.  !!!  I was really surprised that the baby chimp's skull looks so much more like ours than like the adult chimp's!  The flat face, the domed skull, the relatively small teeth.........

Another thing he mentioned is the differences in placement of the opening in the skull for the spinal chord.  When a critter walks upright on two feet, the opening is underneath.  When a critter is quadrupedal, the opening is nearer the back.  The baby chimp has the bipedal arrangement...........

I was already familiar with the concept of pedomorphism -- adults retaining juvenile characteristics.  Adult golden retrievers look a lot more like puppies than do adult wolves.  Drop ears and broad skulls are "baby dog" characteristics, as is extremely friendly behavior.  When we breed dogs to be friendly and trustworthy (less like wolves), we also get a puppy-like look (not necessarily on purpose, it's just what happens when we breed for the behavior we want).

How interesting to learn that we ourselves are pedomorphic!  We are very like adult baby chimps in many ways, and not just in our looks.  He mentioned that babies are usually more curious, exploratory, experimental than adults, and speculated that is a set of traits adult humans exhibit far more often than adults of other species...........


He also mentioned the front-to-back ridge at the top of an adult chimp's skull (to which the chimp's powerful jaw muscles are attached) as something that both baby chimps and humans lack.

Almost a year ago I caught the end of an extremely interesting program on NOVA.  A scientist accidentally discovered that all humans share a flaw in the DNA that enables strong jaw muscles.  (That link is to my blog post on the topic, which details what I remembered hearing, the day after I saw the program.  In the comments on that post, my friend Carolyn kindly offers a link directly to the NOVA program.)

Skulls begin as a collection of bones, which fuse into one as the animal gets older.  The incredibly strong jaw muscles of chimps (and gorillas) have to be attached to incredibly strong bone.  This requirement for very strong skull bones (to support those intensely strong jaw muscles) means that chimp skulls must fuse when the chimps are about three years old.  Brains cannot continue to grow in size once the skull is fused.

The NOVA program speculated that our pitifully weak jaw muscles (in comparison to our chimp or gorilla cousins) makes it possible for our skulls to fuse MUCH later (in our 20s, up to age 30), which makes it possible for our brains to grow and grow.....

The baby-like domed skulls humans retain in adulthood, which house our big brains, might not have been possible without that "weak jaw muscle" DNA mistake.  !!!

I love it when I can listen to a genomics lecture and link it back to what I know about dogs, and what I learned last year about jaw muscles and brain sizes...........  !!!  Many things are wrong, in our modern world, but the ability to be exposed -- SO easily! -- to all of this information is just super. 

This is an excellent time for a curious person to be alive!



Digression -- I am still boggled by that "Gorilla jaw muscles are the size of human quadriceps" thing!  Quadriceps.  *Quadriceps*.   !!!  Whoa.  !!!  End of digression.

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