Thursday, June 29, 2017

Genotyping for the Masses

I remember in the 1990's when the first genome of an organism was mapped out. It was a pretty big deal. It wasn't much later the whole human genome was mapped. DNA sequencing and genotyping continues to get faster and cheaper. Genotyping, determining the specific genetic variants a person possesses, has become cheap enough to draw curiosity seekers in.

Many companies now provide ancestry analysis. Spit in a tube, and for a hundred bucks we'll tell you how many hundreds of years ago that 0.5% Mongolian entered the blood line. Or no, you really don't have Native American DNA. Hundreds of thousands have pursued this curiosity now.

Some companies offer much more for additional cost. 23andMe has a traits and wellness option that looks at numerous traits. The normal, obvious stuff, like eye color, but also less obvious stuff like sensitivity to caffeine and sleep habits. 23andMe nailed these last two for me. I tend towards heavier caffeine consumption than average coffee drinkers and I am not a deep sleeper. These DNA traits do not play well together and thus I really should curb or suspend caffeine consumption.

A host of carrier diseases that can be passed on to your offspring are also tested. Prospective parents might be interested in this. All of mine came back negative. One concern I have is that as we become more comfortable moving around in our genome, it will also become easier to tinker with it. Designer babies? It may already be happening. Huge moral implications here. We think climate change is a threat to our species...

A couple tests that 23andMe performed came with a warning and an opt-in or opt-out. These are early onset Alzheimer's and Parkinson's Disease. Some people may not want to know they are going to go batty at an early age. There is also the issue that once you know this information, it could be treated as a pre-existing condition for insurance purposes and you could be denied coverage or forced to pay a much higher premium. I opted to not be told the results of these two tests for now, a decision I can change later if I want. The raw data is there.

I already know my ancestry going back many generations (northwest European). I could care less if my DNA says I can tell my pee smells funny after eating asparagus. Yes, this is one of the tests. Everybody's pee smells funny, but I had no idea some people are genetically incapable of detecting this. I sure can. So why did I plunk down some cash for this silliness?

I recently learned 23andMe checks the so-called "sprint gene." The gene is called ACTN3, and variants of it code muscle composition. Anecdotal evidence for a long time has suggested I'm a fast twitcher. I was never curious enough to find out for sure by getting a muscle biopsy. Carve a piece of my quad out? No thanks! Spitting in a tube seemed much easier and less painful.

It is ironic that I have fast twitch traits yet shun activities where fast twitch prevails. I'm thinking stick and ball sports, track, or even criterium races in cycling.  I like the long distance endurance activities, such as multi-hour bike and ski races. I tend to ride and train with other athletes that are stronger than I in endurance efforts. I can out-gun them in a 5-30 minute effort, but go past a few hours, I get buried.

Another indication I'm fast-twitched is in caloric consumption. I eat much more than my presumably slow-twitched companions. We go on trips, weigh about the same, do the same rides burning the same calories, yet I replenish with far more calories and still lose weight. Fast twitch muscle is much less efficient in producing power than slow twitch. I feel a bit cursed in this regard, but some of my friends feel cursed with slow twitch.

23andMe makes your full, raw data available online. You can browse by gene name, by traits or even chromosome. Scary how much info is there. They don't sequence your entire genome, only parts of interest, but still a huge amount of data.

Below is screen shot from my results at 23andMe of the ACTN3 variation that encodes a specific muscle protein. There are three possibilities here:
  • T/T - no working copies
  • C/T - one working copy
  • C/C - two working copies
I have C/C, two working copies.  Doubly blessed (or cursed) with fast twitch!

So what does this mean? It's not rare. Nearly 30% of those from European descent inherit C/C. Some areas of Africa see closer to 100% of this genotype represented. That phrase "white men can't jump," well, there's a genetic basis for it right here in this gene, the fast twitch gene. What is rare, however, is somebody with no working copies, the T/T variant, reaching high levels of competition in sprint or power type competition. You must have this gene to climb that last couple percent in performance to compete at a world-class level.

So going forward, does this change anything for me? No, not really.  I'm not about to start weight training and racing crits. I already know I don't excel in several hour long events. One of the side benefits of possessing the C/C genotype is that muscle tissue with this protein is more resistant to breakdown from abuse. I now understand better why my body seems to tolerate weeks upon weeks of junky volume better than others. I will continue to engage in activities that are fun, clear the head and provide a balanced fitness.

Monday, April 24, 2017

Arches National Park with Cathy

[Previously posted on FB 4/24] I made a token visit to Arches NP 18 years ago when visiting Moab. Cathy has never been to Moab or Arches before this visit. Needing a break from the bike, it was a good day to visit the park.
The park closes down hard nightly at 7pm throughout this summer due to reconstruction of all the roads at night. Trail areas will be shut down periodically too. There was no line to get in early this morning. The place was practically deserted! And no trailhead areas were closed yet.
We hit the Primitive Trail off the end of the park first. There were maybe 8 cars there. We hit the first couple arches together, then I went around the Primitive loop solo while Cathy checked out a couple of the closer in arches. I had no idea what the loop entailed. There was one scramble that made me think for a minute, like if I slip, where will I end up kind of thought. There were no people back here. The solitude was nice.
Upon reaching the Double-O arch most of the way around the loop, I finally encountered people. Cathy later said they were unloading by the busload. There was another scramble below the Navajo and Partition Arches, which Cathy didn't attempt. She is 4 months post knee replacement and is still regaining strength. She went out to Landscape Arch though.
After this loop (8.2 miles for me), we went over to one of the Park's feature attractions, Delicate Arch. This was 3 mile round trip hike with good deal of climbing. Cathy felt up to it. Lots of people out now, but there were still parking spots available. After leaving the parking lot, you come around a bend and hear people ask "are those people up there?" Yes. You go up that. Was pretty cool looking, although I worried about how Cathy's knee would like coming back down that constant grade.
Up top you wrap around on an exposed ledge. Cathy said I've gone far enough. Nooooo, only 100m to go and then the arch is right there! Others offered encouragement.
Wasn't quite a mob scene when we first got up there, but the crowd built. We hung around a good half hour or so, did the touristy thing of waiting in line to have a stranger take our picture under the arch. Felt just like the tourists I despise on Mt Washington waiting in line for photo op at 6288ft, except we did not take a train or car up here.
Cathy did very well. Many noticed the scar on her knee and knew exactly what she was experiencing. They had matching scars, one woman on both knees. Cathy hiked about 6-7 miles for the day with upwards of a thousand feet of climbing.
We stopped two other times as we made our way out of the park, at Sand Dune Arch and at the Windows Section. Both had cool features worth stopping for. My tally for the day was about 14mi with ~3000ft of climbing. Maybe not quite a recovery day, but at least I stayed off the bike. Primitive Trail Strava track.

Cathy starting out on Primitive Trail


Cathy and bugs

Tunnel Arch

Pine Tree Arch 
Cathy returning from Pine Tree Arch. Had these first two to ourselves.

Heading out solo on the primitive part of Primitive Trail. A trail weaves through those fins.

Section that gave me pause on Primitive Trail. Slot dead ends, had to scramble up fin to left.

Could one scramble all the way up there? Gave me the chills thinking about it! 

View down slot from Primitive Trail

Side spur out to Private Arch. Hadn't seen anybody in a good while, so it was very private.

Side spur out to Dark Angel. I'm sure others would call it something else...

La Sal's from ridge heading out to Dark Angel

Double-O Arch. Note smaller arch below prominent arch.

Return along tops of fins on Primitive Trail

Primitive Trail 
Side spur out to Navajo Arch

Side spur out to Partition Arch

Scramble up there that stopped Cathy from getting to Navajo and Partition Arches. Not visible from this angle is how deep the slot was along either side of this fin.

Landscape Arch. I remember visiting this one back in 1999.

The narrows heading out to Sand Dune Arch

Cathy at Sand Dune Arch

Playing around in narrow slot at Sand Dune Arch with Cathy.
Cathy heading up to Delicate Arch, with Cathy

Massive bulge of sandstone to scale on way to Delicate Arch, with Cathy

Scenery never sucked on way to Delicate Arch

Cathy doing fine in one of the more rugged sections on way to Delicate Arch

Cathy enjoying some easy trekking on way to Delicate Arch

The two of us on way to Delicate Arch

A cove I saw someone else scramble up to.

It was easy getting up there but not so easy getting back down.

The exposed ledge that Cathy at first refused to traverse. Only a hundred meters or so of this with a 100-200ft drop to the left.

And then just like that Delicate Arch appears with the La Sal mountains in background.

Delicate Arch

Delicate Arch

Edge view of Delicate Arch

Back side of Delicate Arch. Few hundred feet straight down.

Cathy wanting to get out of the wind. There was zero wind until this point, then it picked up to like 25mph. Mild temps though.

Rare instant with no people in Delicate Arch

Cathy coming down from Delicate Arch

Almost down, new knee holding up fine.

Petroglyphs at the bottom

North and South Window Arches

Two of us at Turret Arch

I took the primitive trail around back side of North and South Windows.

View from back side of The Windows.

Sunday, April 23, 2017

Magnificent 7: There were F-bombs

[Previously posted on FB 4/23] When in Moab, there are a few rides that are too good to miss. Yesterday I rode the (almost) Whole Enchilada. Today it was the "Mag 7." The Mag 7 links up several trails near Canyonlands National Park. Many shuttle the official route, if there is such a thing. Although the route has a downhill bias, there is considerable amount of steep, technical climbing along the way.
I did a big ride with Dave in 2013 on these trails. It was a loop and did not hit the lower portion of the Mag 7 route. Today Cathy dropped me off at the top so I could ride all the way back to town, 40+ miles. I thought with the downhill bias, this could easily be banged out in four hours, even with taking lots of pictures.
Cathy is renting a townie bike for the week, working on strengthening her new knee on the paved bike paths that lead out of town. She likes it her but has no idea how hot it gets in summer...
I sampled a good portion of the new Horsethief Trails at the height of land before embarking on the Mag 7 course. These trails were marvelous. Flowy, fast and surprises were rare. Certainly good trails for noobs to cut their teeth on before trying the Mag 7. The trailheads on Rt 313 were packed, but I encountered people only twice in 7 miles on this network.
Starting on the Mag 7, dropping in on Bull Run gives you a good taste of what you're in for over the next couple hours. Everything is rollable if you so choose. I always choose! Temps rose rapidly today, reaching into the 80's, so I was glad it was a hazy day.
In 2013, Dave and I headed back up the trail system when we got to Gold Bar. To continue the point to point ride, I continued on the Gold Bar singletrack which merges into a jeep track up the the ridge. You know those massive red cliffs you drop below heading into Moab while driving on Rt 191? Gold Bar tops out at the highest point on those bluffs. The view was magnificent, pretty much unobstructed 360 degrees. It was a brute to get up there though.
Continuing along the ridge, Golden Spike jeep track is taken. This is where the ride went to shit in a hurry. I was hoping for a relaxing cruise back to town, but the jeep track did nothing but drop off ridge and then go right back up at fall line grades. It sought out many interesting "problems" for jeeps to tackle too, which meant dismount scrambles for me. Glad I wore my new cheap Specialized shoes with sticky Slip-Not soles for this ride! Golden Spike was nothing but none-stop PUDs, pointless ups and downs, in hiking parlance. This wouldn't have been so bad if I had planned on it.
Things went downhill from there. I wasn't going to take the Portal Trail down riding solo (where several deaths have occurred), so I took option B, Poison Spider jeep track. The problem here is it's been pretty dry and numerous, sometimes lengthy sandy patches were essentially foot deep talcum powder that were impossible to ride. F-bombs! I was sipping the last four ounces of water I had for the last two hours. I brought only 90oz or so with me, not nearly enough for 6hrs working hard on a hot day. One of the jeepers did ask me earlier on Golden Spike if I was all set with water. I was at the time, not knowing what lie ahead. The jeepers were pretty impressed I rode all the way out there. I thought what's the big deal, it's less than an hour back to town... It was more like 3hrs. Golden Spike and Poison Spider jeep tracks are probably the most deserving of a "one-and-done" label of any trails I've ridden.
I was so glad when Rt 297 came into view. Been a while since I got myself into boondoggle territory, and today was a pretty good one. I finished with 45mi and 4800ft of climbing in about 5.5hrs moving time. I used both Garmin and Suunto on this ride, as the Suunto does much better capturing the minutia of elevation changes in this terrain and the Garmin does better with distance. Almost a hundred miles and 10,000ft in two days. This trip is going to kill me. 44.5mi, 4800ft, 5.9hrs.

Mustang Trail in the new Horsethief trail network

Mustang Trail with La Sal's in hazy distance

7-Up trail

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Mag 7!

No E-bikes!

Exposure on Bull Run

Slot Canyon on Bull Run

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Rim riding, probably still on Bull Run. Cathy would rather not see these. Sketchy selfie...

This might be on Great Escape trail with the ever present La Sal's in distance

Great Escape

Probably still Great Escape trail 
Great Escape trail? So much fun bombing this stuff with near continuous downhill slope. Heavy braking was rarely needed.

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Heading up Gold Bar jeep track

High point of Gold Bar, looking north on Hwy 191 towards SLC

View southeast from Gold Bar high point, around 5500ft elevation.

Slight zoom on the La Sal mountains.

View south from Gold Bar rim with Colorado River in distance. Ride pops out somewhere down there. Had no idea what lie ahead.

There were surprisingly few jeeps out. Encountered only three moving caravans and a few stopped. Despite my pathetic pace and ability on this terrain, I could still move along much faster than these guys.

I stopped for 10 minutes to watch this guy solve this problem on Golden Spike. Had a couple spotters giving wheel feedback. 
Almost there. That rear tire had to drop before rolling over.

Slick rock section of Golden Spike jeep track. This actually wasn't too bad of riding, except it still threw some ridiculous grades at you.

Golden Spike in a slickrock wash

Oh, if it just stayed like this the rest of the way! But a whole lotta suck was coming.

Tops of the La Sal's from Golden Spike jeep track

One of my favorite views from the ride on Golden Spike jeep track.

Then there came sandy section after sandy section on Poison Spider jeep track. Fine pixie dust kind of sand. Sucked your soul dry trying to ride it. Should have taken the Portal Trail down!

Brief non-sandy bit of Poison Spider

Heavenly sight for a weary soul, the final Poison Spider switchbacks down to Hwy 279.