The Selfish Gene

The Selfish Gene by Richard Dawkins

An ebook is available from libraries. Audiobook is available from audible and we have a paper book. I listened to the text to speech of the ebook. The simple thesis of this book is that "genes" are the primary unit of genetic propagation. Organisms are the vehicle for this propagation to get carried out. The author also admits that "cooperative gene" would also be a valid title for the book. 

The text provides examples and additional stories to carry out these points. Having errors in the replication is key to the process. This lets new things appear and change. There is a long discussion of the "prisoner's dilemma" and how that is related to genetic propagation. People may have many descendents. A 20th generation descendent many not have any genetic material that came from this ancestor. However, social knowledge and changes could be passed down.

Though the book has been updated in recent years, some of the original content is present. There is some mention of computer power and resources which is totally out of date, but still makes it's point. (It can be a bit jarring when it is followed by mention of the author getting his genome sequenced.) The book seems fairly long for the points made. 

How Life Works: A User’s Guide to the New Biology

How Life Works: A User’s Guide to the New Biology by Philip Ball

Everything you thought you knew about biology is wrong - or at least inadequate to explain how things work. Biology had drifted towards a "genetic determinism" approach. It was assumed that genes were like computer programs. If we understood the genes we could understand everything. We could just manipulate the "code" to get any desire we wanted. However, biology is not that deterministic. 

It was thought that DNA is primarily for coding proteins. Non-coding DNA was seen as "junk" that may have held a legacy purpose, but is not useful today. However, it is not that simple. Much of that non-coding DNA has distinct purposes that define how organisms develop and behave. 

In general, genes are probabilistic, not deterministic. There are many factors in play. Cells are often guided by neighboring cells in their behavior. Epigenetics, neighboring genes and environmental conditions all can play a role in development. When comparing life to computers, it is much more like a learning model than a predefined algorithm. Or perhaps we could consider it more like the development of an unplanned city vs. central planning. There is simply a lot we don't understand and probably a lot more "chance" involved than we have suspected.

The Son Also Rises: Surnames and the History of Social Mobility

Your name can tell a lot about you and your economic prospects. Theoretically, in an egalitarian society, all families would revert to the mean. Those that were rich would have offspring that were somewhat advantaged, but over the generations they would be similar to others. Similarly, the poor would have the opportunity through education to increase their stock. However, in looking at surnames and associated markers of prosperity, there is an unexpected stickiness of prosperity.

Many of the tests done involved correlating names with indicators of "success". This was somewhat limited by the available sources. In Britain, the authors looked at Members of Parliament, students at Cambridge and Oxford, and probate records. The focus was primarily on the more rare surnames. It was found that surnames that were overrepresented by wealth markers tended to stay over-represented. Their reversion to mean was slower than would be statistically expected. This was found even when large investments were made in education. Similar results held in almost all other countries, even those that were supposedly very egalitarian. Sweden provides free education and subsidizes living expenses, yet the rich continue to hold their positions. Even after the cultural revolution in China, the elites came back. Similarly the descendents of samurai in Japan continued to show privilege long after the positions were abolished. These factors seemed to show something even beyond genetics or nurturing.

The authors did acknowledge there were some challenges to the methodology. Some people would change their names. (Though this relatively small occurrence would often reinforce the elite positions.) It can also be difficult to get accurate data, with many places recording things differently (and the same places have different data over time.) 

There were also some interesting results that appeared for certain groups. Those with European French surnames in the US tend to be underrepresented as doctors. (Perhaps because it was the poor that most often immigrated.) Jews are over-represented among the elites. This may have started as they had widespread literacy before others, yet it continued after the world caught up. In Ireland, there was a sorting out of Catholics and Protestants with people often sorting to their class group.

Analyzing groups as individuals is often subject to controversy in our world. It does provide some interesting insight into different values and changes among the people of the world. 

A Brief History of Everyone Who Ever Lived: The Human Story Retold Through Our Genes

We can learn a lot about history by looking at DNA sequences. Advances in technology make it much easier to sequence DNA that we can find in long-dead remains.  Other "human-like" species have existed and mated with humans, yet they no longer exist today. However, there are still traces of their genetic materials. Europeans and Asians have some Neanderthal genetic material, yet Africans seem to lack it. We can even analyze the distribution to determine which side tended to be females and male in the early mating. 

This book is a discussion about what our genes can and cannot tell us. A lot of what we can know involves comparing DNA to known sources. What we have trouble knowing is the impact certain genes have on individuals. The news will often report that scientists have discovered a gene for a certain trait. However, this simply indicates there is a statistical relationship between the gene and trait. It may be fairly useless. A large percentage of incarcerated people may have a gene. Yet, if the gene is also prevalent in a large percentage of free people, it doesn't tell us much. Genes will often work together with other genes making it unlikely a single gene will indicate much. We can consider this the start of scientific research rather than the end.

Genome: The Autobiography of a Species in 23 Chapters

Matt Ridley is very strongly pro-science, yet is not afraid to ruffle feathers or bump against orthodox views. Although Genome is over two decades old, he picked a writing approach that makes it still worthwhile. He takes us on a "tour" of the human genome, going chromosome by chromosome.. For each one, he picks something that is relevant. It may be a disease that is associated with it. It may be a well known gene associated with a specific location such as Huntington's disease. Or it may be looking at a location where researchers thought they found something interesting. The history is still interesting even as many things have changed since the book was written.

Family Gene

The author of Family Gene has a rare genetic mutation that appears only in her immediate family. It seems to be sexed-linked, only passed down from mother to child. However, men are more severely impacted. It leads to bloating and excessive fluid production and an early death - though typically after child-bearing years. She is lucky enough to have connections to a medical research community that is studying her condition and seeking out a cure. Alas, for now all they can do is small treatments to help lesson the impact.
during much of her twenties she was quite a rebellious type (to a degree impacted by the decline and early death of her father.) She tried to get health insurance, however, was unable to due to a benign heart murmur that had been diagnosed earlier. This makes a good case for a better socialized medicine. She also found she was nearly completely Ashkenazi Jew. The narrow gene pool has allowed various mutations to propagate. (As a side, she also talked about the "blue" people of Appalachia who had a recessive trait that was passed along a tight-nit population.) You wonder how many other odd conditions are out there that we don't know about

The Gene: An Intimate History

The history of the understanding of DNA and genetics is a fantastic tale of science marching forward and backwards in a quest for knowledge. There were plenty of detours and missed opportunities in the development of understanding of genetics. The Greeks had many ideas, most of which led scientists down the wrong paths. Mendel had a clear understanding of genetic crosses through his pea experiments. However, his work was ignored for decades due to his lack of "credentials". Darwin had some keen insights, but also had some guesses that turned out to be totally wrong. Eugenics appeared to be to the wave of the future and a way to help "improve" the human race. Then the Nazis adopted it, and it become verboten. (Today, however, it is carried out in a more "unofficial" format with genetic testing and elective abortions of "defective" fetuses.)

In "The Gene", the author uses his family's history of mental illness to weave together a history of knowledge of genetics and the human applications of this knowledge.

Today we have learned a great deal more about how DNA encodes "us". We also have the power to make changes to the genetic code. We have used this power to make extensive changes to plants. We can also make changes to animals and even humans. This gives us great power, but also poses a great risk. Many genes work together to produce a certain outcome. Research is primarily through a "guess and check" approach. We try to change certain genes in an animal model to see the impact. We may look at various people with a similar condition and try to find similarities. It may be tempting to "turn off" a certain gene that leads to a disease. But what will be the ramification? Will this also turn off immunity to a future unknown disease? Will that cause some unknown negative problem in the future?

The power to make genetic changes is perhaps one of the most scary abilities we have today. People are having fewer children and using more medical assistance and genetic screening. Will we accidentally screen out an unknown important mutation that is needed for our species' survival? Will we create a homogeneous society that differs only superficially? Or will we accidentally hit the self-destruct button? The state of the art in genetics lends itself towards a justification of an intelligent design. We have the ability to manipulate genes. Why not create entire species? Are we the first to do it?

I could envision a past world where dinosaurs wanted to be the best dino-league athletes. They engineered themselves to be larger and larger until they reached the gargantuan sizes of the day. This was wildly successful for a time. However, problems arose when the environment changed in unexpected ways. The cultural bias to bigness was so prevalent that they ended up having a dino-war rather than adapting to smaller sizes. Eventually they became mostly extinct. That is, all except a renegade group that decided they wanted to get smaller and smaller. They figured out how to change their DNA to shrink them to be smaller and smaller. They then used the genetic knowledge to create other organisms to house them. Other animals were merely biological "houses" were these beings could live and reproduce. They created their harems and started reproducing like crazy. They were able to get the last laugh in as they "dominate" the big species of today.

What will we humans do with our genetic knowledge? Will we try to do too much before we know enough? Will we cause irreparable before we know what we are doing? Or are we doing things at the proper pace now. We have power, but we are only beginning to understand. I hope we can make good decisions.

Friday

Friday mixes some of Heinlein's early and late career style. It is a space travel adventure, but also a sociological critique. The eponymous Friday is an "artificial person". She was created by combining the best bits of DNA from different people to create a "super-human" embryo. She works as a courier, delivering special items (often in a secretive navel case). She knows little about the true purpose of her mission, and is thus not able to reveal much when tortured. She longs for a normal life (in one of those bizarre Heinlein familial relationships.) However, after joining the family, she is offended by the prejudice shown to other races and to artificial humans. (The New Zealand family is against a marriage to a primitive Tongan, however, they would have been ok with a Maori, because they are "normal") She gets booted, and goes back to other jobs before getting the big job as a courier for the seed of a ruler. However, she realizes she will be killed after delivering, and jumps ship with the help of her artificial human guards. She then goes on to live happily ever after on the "Botany Bay" planet colony.

So much for the plot. It is not bad, but the real power of the novel is in the world that is created. This near-future world has been balkanized in to many new states (like independent Texas and California.) Multi-nationals also play a strong role, often being more powerful than the states - in part because they don't have a distinct area that can be attacked. California is democracy and equality taken to the extreme. The referendums can be used to correct any "wrong". (People were upset that people with bachelor's degrees earned more than people without, so they legislated that everybody would receive a degree as soon as they graduated from high school - and then later grandfathered in people that graduated a long time before.) These places also have many laws that are not enforced, thereby degraded the remaining laws. Artificial people have a strange role here. They are often given false birth certificates, usually from places that have been destroyed (like Seattle). People expect them to be easily recognizable as artificial. However, in reality, they blend in with normal people. They however, become a vehicle for rhetoricians that need some foil to advance their cause.

He also describes a balmy planet, with near perfect weather, flora and fauna. It becomes an ideal retirement community. And in order to enforce that, voting is restricted to those property owners above the age of 70. Younger people serve long periods of indentured servitude, thus providing services at much lower wages than would otherwise be required. (Hmm... Many examples of similar situations could be pulled from the earth today.)

In the end, the lead character finds pleasure in the simple life of being a mother and a homemaker on a rather primitive colony. Perhaps this slow pace is a utopia from the modern, fast-paced world.

In Pursuit of the Gene: From Darwin to DNA

[August 2009] I wanted to be interested in this book, but I kept finding myself putting it down, and only with much effort was I able to finish. The writing style is fairly accessible. However, the content seems to be a little too compressed. There are many players involved and many bits of biology to keep track of. The subtitle may also be better stated as "Darwin to DNA (exclusive)" The discussion of DNA is passed over quickly in a final epilogue.

The book approaches science through a very personal approach, putting forth much of the "behind the scenes" relationships and competition that took place to arrive at the better understanding of genetics. The story is built through the history of the intertwined relationships of many of the great biologists, starting with Darwin and going on to nearly the present day. The focus is on a few significant players, providing at times fairly detailed biographies of both personal and scientific life.

Unfortunately, it falls short in trying to do too much. With so many people covered, it became difficult to sort one from the other. The details of their discoveries also was jumbled and not explained in clear detail. For somebody with an existing knowledge of the key discoveries and discoverers, this book would likely provide enjoyable insights in to the background of the discoveries. However, as a human biography or an introduction to the origins of genetics, it falls flat.

Basics of Genetics

Basics of Genetics does exactly what is advertised. It presents a comprehensive overview of the basics of genetic principles. It does not go overboard in to the detailed minutia of modern genetic theory, but does provide a solid grounding in the "evolution" of genetic thought.

Having spent significant time immersed in advanced genetics scholarship, I was not expecting much from these lectures. However, I was pleasantly surprised. She did an excellent job of explaining the basics in an easily understandable manner (with plenty of analogies and examples.) I came away with a much clearer understanding of things that I thought I already understood, as well as knowledge of ideas that I "took for granted" rather than trying to understand. The analogy of the "Rube Goldberg cookie making machine" is still stuck in my mind.

Double Helix

It is tough to get involved with this book. The characters seem to be all caught up in some emotional wrongs, yet at the same time it is hard to feel sympathy towards them. Little attention was paid to details (tennis scoring anyone?), and the genetic basis seems somewhat plausible, but not very convincing. The characters also seem to come across as "what an adult would think teenagers would be if they could do what they want". Aside from all the plot and character issues, the book does move along well with some suspenseful pacing. If only the endgame of the suspense were something worth waiting for.

Monterey trip

I did the bicycle trip to Monterey for the genetics retreat this year. I thought I had planned well, but then I got off to a late start. After a couple miles out, I realized that the two water bottles I put in the freezer "for a few minutes" were still in the freezer. At least I had the one emergency water bottle in the back. I guess that would have to do. Luckily the weather was just about perfect. Not cool enough to justify a jacket, nor hot enough to cause a lot of sweat.

The trip to Los Gatos was uneventful enough. Again, this year, I followed the signs to the Los Gatos Creek trail instead of taking the quick entrance on Santa Cruz. D'oh! Eventually I went through some alleyway over a few bridges, and finally on to the trail. The trail was one of the least fun parts. The crushed limestone gravel just slows things down, and I was unable to get traction to climb up some of the steep hills, thus I had to wheel my bike up. From there it was up around the reservoir on Alma Bridge (stopping at one little park with an outhouse), Old Santa Cruz and Summit, and then down San Jose Soquel. The climb is extremely nice - mostly shaded, not so steep that you need the lowest gear, but steep enough so you are not climbing forever. The pavement is also in great condition. The decent is also great. Smooth pavement, and just about the perfect mix of grade and turns to allow fast speed without much breaking. (The only downside was some tree work at the end of a downhill. The flagger even apologized for destroying my momentum.) There is a nice park near the bottom of the hill with water and a bathroom.

Then on to Soquel Road for a long haul. I saw a hole-in-the-wall donut shop somewhat near the community college, so I stopped in for an Apple Fritter. Yum. They didn't have much a of a selection, but the fritter was good.

Around Rio Del Mar, Soquel makes a curve, and I always seem to get confused. This time, I found myself on Huntington, and decided to continue on it. It has hardly any traffic, but some nice little hills. From there, it was a hop down Valencia to Freedom. I continued on Freedom to Watsonville. The first section of Freedom was mostly farmland (lots of apple orchards. (I recall passing a "martinelli" street.) Then it turns industrial, and the pavement becomes absolutely horrid. Eventually, I ended up in downtown Watsonville (and passed by a park with a water fountain) A couple metro buses follow this route, so it could provide an alternative.

From Watsonville, I went over the bridge to Pajaro, and then continued on Salinas and eventually to Elkhorne. This road has very little traffic, with some shaded sections and hills. It makes for a much more pleasant ride than Highway 1.

Then I got to Castroville. Or almost to Castroville. At 156, a sign said the right turn was towards 1 north. I thought that left must then lead to one south. Even the long wait for the left turn signal was not enough to convince me otherwise. After going for a little while, I had a hunch I was going in the wrong direction, but with it being around noon, I had a hard time judging by the sun (and my GPS was gone...) After a little while I was convinced it would be good to make the next right turn. Only problem, is there wasn't a right turn for 4 miles! Finally, I reached a right turn to 101 at Prunedale. I remember this place from the MST 55 bus, so I figured it was not the direction I wanted to go, but I could quickly take the first right to get back towards Castroville.

101 had a nice wide shoulder, and a couple traffic lanes, making it a somewhat more pleasant than 156. Part way down 101, a highway patrolman stopped me, and advised me not to ride on 101. I asked him if it was ok to ride there, and he said it was legal, but there were lots of large trucks and unlicensed drivers and it was dangerous. (Hmm, wouldn't the unlicensed drivers be on other roads, too? And there are plenty of large trucks moving at fast speeds on other roads - most with narrower shoulders.) However, I was clearly headed in the wrong direction, and wanted to get on to Monterey, so I asked him for the fastest way there. He pointed in the route that I was considering, back to Castroville. D'oh! (And his recomendations included a narrow road and then a high volume, high speed road with lots of trucks... Sigh)

So it was back down Blackie road to Castroville. Blackie has a little bit of shading. Which made it better than the heavily exposed other roads I was traveling...

Finally I end up on 183, and notice I'm heading towards Salinas... Again! D'oh! I see a turn off (Cooper) that seems vaguely familiar, and follow it down to Blanco. I remember that one from a previous trip back from Monterey. From there its on to Reservation and then Imjin. Then through CSU Monterey Bay and under Highway 1 to the bike path. I actually took a different underpass that took me to the 'empty' road on the beach side of the bike path. Its a little more pleasant, being a greater distance from the freeway.

I eventually made it there, 2 hours late and very sunburnt. D'oh! The 75 mile trip ended up being about 100 miles.

There was a professor (Stuart Kim) and one of his students that had also biked in. They went through Gilroy and over 152. When I went to my room, there was a do not disturb thing in the door. When I game back with my bike, one of the bikers appeared there. It turned out my roommate was in their same lab, and was letting them borrow the room to shower because her room was not ready yet. I finally had a nice shower and realized I was a little fried. The bathtub was also a slow drainer. D'oh. This room was not on the beach side, so I didn't have all the load beach waves at night... Instead there was highway noise.

The next day, I had visions of going down to Big Sur. However, it was a little further than I had anticipated, and I was a little slower than I hoped. I also got a little twisted up on the way to Carmel. Going down Highway 1 in to Carmel, I decided I would not repeat that route on the way back. (I had done that last year. It did not look like a fun hill to climb, especially with rush hour traffic.)

Highway 1 south of Carmel was uninspiring. The heavy traffic made it loud, and the mixture of wind and hills made for a challenging bike ride. Perhaps the greatest challenge was the fact that it was an 'out and back' route. There was no other road to turn on to make a loop back. I would just be going on the same road that I took there. And the scenery was just cliffs, hills and beaches. It started to get old.

So, around mile marking 62 (Rocky Point restaurant), I turned around to head back. There I realized that the bits were I seemed to be making good speed were really due to a tailwind. D'oh! That left me with a nice headwind going back.

Near the turnaround, there were a group of beachfront estates - it looked like everyone was for sale - for about $6 million dollars. The multimillion dollar homes in Carmel Highlands looked a little more appealing, but I think I would pass on the beach view... Just a little too loud for my tastes.

On the way back, I went by Carmel's beach, through Pebble Beach, and around the end of the '1X' bus route only the coast and eventually to the bike path. With all the detours, the total trip was somewhere in the 40-50 mile range.

For the trip home, I decided to try to be as direct as possible. But things can sometimes get in the way. I took the Bike Path, then continued on to Del Monte. Near Marina, I really had to go to the bathroom, I jumped over the railroad tracks to Marina Library. Then I got twisted up, going out to the Reservation beach before eventually finding my way back to Del Monte/Monte. Then it was on to Castroville via a road and bike path that connects Nashua to Merrit. I tried to hunt again for a public facility, but I just seemed to see industrial areas. Castroville also seemed rather small for the population figure given. Finally I crossed the highway and found the "artichoke capitol" (75% of the US artichokes come from here according to wikipedia). I eventually found the Castroville library - had to ask for a restroom key ("due to vandalism").

From there I continued on Merrit Street, which eventually came to 1. This section of Highway 1 is not horrid, but not fun. It is loud with a lot of traffic, and it goes close to the coast, making for lots of wind.
Shortly before reaching Jensen, I noticed a lull in traffic, and thought I might try to make a left turn to go through the strawberry fields. However, when I got closer, there was a steady stream of traffic, so I decided to continue onward. Then the road became a freeway, with a bikes must exit sign. (I never understand why they make bikes exit when it becomes a freeway - this seems to make it safer for bikes. The traffic splits in to two lanes and the shoulder gets wider. And exits are to the right rather than forcing left turns. Oh well.)

I noticed some "Pacific Coast Bike Route" signs, so I attempted to follow them. This directed me down Salinas Rd. Then a sign
pointed left, so I dutifully turned left at the next intersection - which turned out a private road for a couple businesses. Then I realized it was pointing to the next street, so I eventually made it to the right location, and kept going down Salinas as directed. This lead me through downtown Watsonville, but then the signs seem to have failed me. I continued going straight on the road. But eventually it forked, without a sign.

I continued on Main Street. But, eventually, it entered the freeway. So I followed along the parallel road (westgate). It eventually turned in to Larkin Valley. This is a nice road with rolling hills and very little traffic (but also very little tree cover) Eventually it crossed over Highway 1, and became San Andreas. And right afterwards, it intersected with Bonita, where I found the trusty "Pacific Coast Bike Route" sign again. This lead a short bit down Bonita to Freedom and back to Soquel. Then I continued down Soquel to Porter which becomes San Jose Soquel. I stopped at the park there to 'refuel' for the trip up the hill.

San Jose Soquel seems much longer on the way up than the way down. It really does go past the 10 mile marker. There were hardly any cars going in my direction, but a decent number going the other way (early commuters heading back home?) I had managed to break out a nice sweat by then. Once I started going down the summit, the temperature jumped up noticeably.

This time, I decided to go down Old Santa Cruz Highway all the way (instead of Aldercroft Heights.) It was a fairly nice decent. Good pavement, hardly any traffic. I noticed a VTA bus just ahead of me on summit. I thought I would have a chance to outrun it, but some of the intermediate hills did me in. On the way down, I found myself breaking a little more than San Jose Soquel - partly due to the sun (I just couldn't make out the road.) I road on the shoulder of 17 for the brief bit between the end of Old Santa Cruz and Aldercroft Heights. The shoulder has a few real bad patches there. But, there is still plenty of room. And the rightmost lane is actually an 'exit' lane, so there is plenty of buffer.

After jumping on the Los Gatos Creek trail, I had wished I just stayed on 17 to Los Gatos. To get to the trail, first you have to go down a steep gravel hill. I tried riding, but eventually walked down it. Then up a hill, then down a hill. All pretty much need to be walked, unless you are good with a mountain bike. Yuck.

From there, it was the direct route down Santa Cruz to Highway 9. I had planned on continuing down Saratoga-San Jose to Prospect. However, I got a red light at Pierce, with another car in the left turn lane, so I decided to take that shortcut through the Prospect. I found the right streets, with only one little detour (through a "no outlet" sign I didn't trust, which ended up being true.)

I had already gone through all my water, so just decided to zoom towards home. Eventually made it there, and quickly guzzled the two water bottles that I had forgotten (somebody had placed them in the fridge.)

Trip there was a little before 7 am to 3pm. Trip back was between 10:30-11am to 5:30-6:00pm.

As for the Genetics conference, the talk I found the most interesting was on "barcoding". The goal is to allow quick, cheap tests to determine the identity of species of plants and animals based on a quick DNA sample. The tests have already been used for identifying new species among similar animals in Costa Rica. The speaker envisioned a $2.50 device that would allow for identification, along with a 'tax' that would help support the scientific research and classification. (Somehow, I see the $2.50 device much more likely than the research tax.)

There was also an interesting panel on consumer genetics companies. Should people have access to their genetic information, and what are the consequences. Will some of these super cheep sequencing technologies come aboard? (And not discussed - will this amount to anything? Or will we discover that were missing some other huge aspect of the genetic system?)






View Larger Map

Above is a rough version of the route I took. There were a few additional minor detours that are not included in the map. Also, the 'routing' on Highway 17 was actually the Los Gatos Creek trail, while the routing on 1 was a combination of Beach Range Road and the beachfront bike path.