My Latest Genome SNP report from DeCodeMe

This post is an update on my SNP genome scan report in which there has been a few developments. It came about because my dad (Bob Marshall) had his 80th birthday last week and we made a detailed report on his ancestry based on DeCodeMe. By the Y-chromosome he was related to Somerled the Viking-Scottish 12th century king (as are millions of other caucasians). However, I noted the high risk he has for macular degeneration (5x, 46%). This rang a bell because his grandmother (Jessie Boneham) went blind after "she had her cataracts removed but the operation didn't work" suggesting retinal disease after age 85 years. Anyway I looked again at my age related macular degeneration risk and see a lesser but elevated risk (2.88x, 23%). Last month my eye exam was normal except for early arcus senilis and slight refraction problems. I'll continue with a two yearly check. This year I decided to seriously attend to my blood pressure (erratic and about 20mm above ideal levels if not treated) and also my cholesterol. My SNP risks reflect a 50% risk of hypertension, as well as diabetes, obesity and heart attack (although modestly elevated). Good news is that my risk of muscle damage from my statin is low so I can take these with impunity. My recent blood pressure readings are graphed in one of the documents on the web site. An episode of angioedema caused me to change my ACE inhibitor to an ACE receptor blocker and so far I have not had any more side effects.

You can read my full SNP report plus other health reports here: http://www.bajama.mine.nu/~barry/decodeme/ . I also include an AVI file showing a movie of my coronary calcium CT scan and you can go into the directory below to see my actual raw SNP data in case you want to research it. I don't know what use this information is but I do want to hold true to my idea of a public health record. More and more people care less and less about this type of data - its becoming so common.

What else is new? Well, I am saving up to have my total genome done. I would also like to do my whole family, but the Western Australian DNA bank refuses to store the DNA at present. They are so precious that they only do storage for bona-fide research projects, not for people like me who are just exploring their own family. So I may just keep it frozen in the back of my -80C refrigerator at the H.pylori Research Lab.

So much data privacy - so much wasted value - I opted out and put my genome on the web here

Time and time again my research has been slowed down by difficulties accessing research data. Some groups are determined to make it more and more difficult to access data for research. Data mining - I don't care as long as there is no malicious intent. Congratulations to the USA government for introducing the non discrimination for genetic data act. This means that US citizens need not worry about higher premiums on the basis of their genetic code. In Australia where we have free universal health care, and private medicine if you want a premium convenient service, we should have no serious concerns about health insurance discrimination.
In the meantime, I am sharing my genetic code profile. This was quite an expensive effort but the number of disease related information items increases by about 6 per year. Over the next 20 years I expect to see 120 diseases and risks laid out for me in the report.
You can look at my genetic report here:
Have fun!

make a Conference Trip from Australia to the USA - Without Killing Yourself!

In April this year I might have found the best combination for a trip to the USA from Australia incorporating an important international conference and several lectures. Try this schedule if you can.

1. Allow for a low activity week prior to departure. You will likely have visa and travel arrangements, family visits and last minute supplies to organise.
2. Make certain that all you computer backups are be up-to-date.
3. Test that all your essential files are accessible via the internet while you are away. With "cloud computing" you can now have a shared folder to use from anywhere. I use "dropbox" and have a 50 Gb space there. Just watch out if you go to China, you might be blocked by the big firewall. With DropBox you can use a folder you have already created, but cannot access the web interface.
4. Subscribe to a "hotspot" wireless network so that you can check email in the airports and coffee shops without incurring Telstra roaming fees (I find Boingo is the best).
5. For non-electronic communications, set up paper mail forwarding, letterbox checking and junk-mail removal by the your neighbours. Also notify neighbours you will be away.
6. Delegate academic tasks requiring deadlines to trusted colleagues.
7. Pay cellphone bills and top up credit cards in advance so that your telephone doesn't go off-the-air before you return.
8. Carry a secure thumb drive with your recent work on it.
9. Check that you have done the ISTAR USA visa form on-line (this is even necessary for Aussies. We are descended from convicts remember!).
10. Don't drive yourself to the airport. You will be too rushed. If the taxi service is not 100% reliable, have a backup plan. Preferably, pay the extra $50 to have a private car service take you to the airport.

In the USA, address the issue of Jet Lag by arranging a schedule as follows:

• When arriving in the USA from Australia, try not to do anything critical for at least 4 days. If you immediately attend a conference you will sleep through it and learn nothing so your whole expensive trip will be wasted. Therefore, one strategy is to enter via Los Angeles on Monday or Tuesday, then continue straight through to Las Vegas for 4 days rest (Wed-Sat).
• Day 1-4: Sleep as much as possible, swim and walk around the streets for exercise and experience the sunny climate which helps you change your sleep/wake cycle. You don't have to gamble but Vegas never sleeps so at 3 am you can go out to eat. The Hotels are excellent with world class variety shows. Also, there are great outdoors attractions such as the day trip to the Hoover dam. All the top US technology stores are available and fast internet is the norm if you need to work.
• Airlines in and out of Las Vegas might be less reliable as they are the cheap flights. Also they have luggage limits sometimes.
• Day 5-9, (Sat-Wed): Travel to your final conference destination.
• Maximise your conference value by staying in the actual conference hotel because you can take a nap in the middle of the day so as to be fresh for the afternoon sessions. You also save bus travel time and/or cab fares. When looking at the actual extra cost, $150 per day extra is probably money well spent.
• Day 9-12, (Thur-Sun): Take a second break incorporating the weekend. This might involve a travel day and a rest period in a city where you can visit relatives or friends.
• Day 13-17 (Mon-Fri): These are more work days travelling to visit colleagues, conduct business, give seminars etc.
• Day 18-21 (Fri-Sun): These are final wind-up, consolidation and recovery days in preparation to travel back to Australia. In my case this involves one day of travel back to Los Angeles. Then during this weekend I recommend staying in Burbank - actually the Residence Inn - where you can have a hotel suite, free internet and free breakfast. While organising for travel back to Perth, do some final shopping, see a movie, enjoy the climate and throw away anything you don't need (especially conference materials). On the Sunday morning, my "must see attraction" is the Page Museum in central LA which incorporates the La Brea Tarpits which have trapped hundreds of prehistoric mammals. The LA Museum of Art is next door with a nice restaurant. Finally, allow two hours for a visit to Fry's Electronics, the world's largest electronics and computer gadget shop (it has 68 checkouts).
• Day 21-22 (Sun-Tues): Fly back to Australia. Realistically, four hours of low intensity laptop work, reviewing manuscripts etc. might be done during the trip. However, dry eyes and poor posture often limit this to less. Don't start something you cannot finish in the time available - you may not get back to it for several weeks. If you plan laptop work make sure you charge the PC before leaving. Sometimes the older planes do not have a compatible power connection, even on business class.
• Day 23-25 (Wed-Fri): Only essential work duties are possible. Don't expect to safely perform high level patient care or intensive administrative activities. My typical day starts at 4-6 am with 2-3 hours of email and document work, then 4 hours at the University from 9 am -1 pm, then a 2 hour nap after lunch and then an evening event from 6-9 pm.
• Day 26-27 (Sat-Sun): Perform activities necessary to follow-up from the international trip and revert to normality.
• Day 27-30 (Mon-Wed): Allow for a gradual return to normality. I notice that a depressed mood can continue until 12 days past the day I left East Coast USA. Thus, on the above trip, which allows for three final recovery days in Los Angeles, I am completely normal one week after arriving back in Perth.

There is often a temptation to extend a USA trip with academic activities at the end. My experience is that I am looking forward to going home by three weeks and I always regret the fourth week away. So in reality, a conference in the USA requires at least 14 days of related activity and 7 days of recovery time. If extra lectures are planned then allow a 50-50 split between R&R and work or you will burn out. Tomorrow I leave for a three week USA - Europe - UK - Asia international trip with just a carry-on cabin bag. My best record for this is 5 countries on three continents in three weeks but it was gruelling and my follow-up afterwards was very inefficient.

Words to avoid in presentations and in speech

This month I have decided to go public with my list of “meaningless words” which should no longer be used in public, especially not in meetings or presentations and never on TV or radio. Here are the ones I recall today.

1. Basically
a. This word has become a favourite of scientific people especially when they are answering questions. I am also guilty. Example as follows - Question: If the DNA is copied until the primer just falls off, how is it that all the pieces of DNA end up exactly the same length? Answer: Well, basically, you are almost correct however, only the first copy gives a random length. After that, basically, the primer in the next cycle has to start 637 base pairs from the start point of the first copy. So, basically, all except the first copy are the same length, basically 637.
2. I mean
a. This seems to be used as a spacer between sentences, where the speaker continually likes to embellish details and add ideas. I mean, just as one would normally give the listener person a chance to talk by leaving a short gap in the conversation, by using “I mean” the gap is stolen back so that the normal person might not get a word in edgeways. I mean, let’s say that it was you being the listener, and you are a nice polite person; I mean, like Marj in the Simpsons. Then you never have a chance to speak because ...
3. Sort of
a. A vague term implying that the speaker has not put any thought into the discussion and is sort of making stuff up as he goes along. This seams to be common in presentations from young artists.
4. Yeah
a. Australians have become adept at placing this word in the middle of sentences as some kind of emphasis. I think it is very common in interviews with surfers; yeah – .
5. Absolutely
a. Television personalities, especially on gardening shows, continually say absolutely. Then the show “Absolutely Fabulous” started up perhaps as a send up of this trend. Recently it has been used more and more by almost everyone. By adding this word, a very vague concept suddenly becomes absolutely correct and proven beyond all doubt. Also, other words can be added to it, especially “fabulous” to make something rather mundane and boring into something apparently exciting. Take the concept of picking up handfuls of animal poo. We don’t have smellovision yet, and the warm temperature of a putrefying heap is hard to transmit to the gardening audience. But I can call it compost and say how this material is absolutely the best thing for your garden. How absolutely fabulous it is to feel the warmth as you thrust your hands into the pile in order to experience nature as the good bacteria convert biodegradeable organic material into absolutely perfect plant nutrients. Actually, it sounds rather attractive as I write this.
6. Umm
a. A non word, also used as a spacer to stop other people butting in. Luckily there is no need to use this on TV interviews because a smart editor will cut out all the wasted time anyway, so as to add more content, or another “non umming” person to the time allocated for the story.
7. Like
a. This word is more often used by teenagers – or even myself actually – as emphasis in a story. But it is used rather informally, among friends, with alcohol on board usually, and often as a preamble to an acted out part of the story telling. I am having trouble explaining it but here goes. Just say that I am telling you about a scene from the movie Avatar. So the main actor Sam Worthington is just a dumb marine so he’s like, “I need to walk again so I will do anything to pay for an operation”; but Sigourney weaver, she’s like some kind of genius professor so she’s like “don’t break the machinery you dumbass!” etc.
8. You know
a. Everyone uses this Phrase, again a spacer to show that you probably don’t know all the facts but what you say is probably about right. Of course, as the brainy listener, you probably have more information or already have heard this story, but if you do know it you would not be so rude as to correct the speaker or embellish his own story. You know.

I think it might be fun to add a few more of these and give funny examples. It would be good practice for a screen writer in a sitcom. My son reminded me of a program we used to have which converted normal speech to “Jive” which was a kind of black American street gang speech which most Australians would hardly ever hear but probably rappers and people from Los Angeles might be familiar with. Time is up – I can’t spend my life just doing a blog. Back to real life.

Singapore Airlines wins Hand Towel Stakes: Secret Technology Revealed

Nobel Laureate's Travel Log: Hot Towels! Who would have thought they were so difficult to get right. The best hand towels are from Singapore Airlines. The luxurious cotton towels arrive hot but not scalding, damp but not dripping wet and are very lightly scented. In comparison, Qantas towels are tiny scraps of material with no pile on the towel, usually dripping wet, and often too hot or too cold because they don't have enough substance to retain any heat during distribution. Emirates towels are a little better but no-where near the SA standard. Cathay Pacific are close but not quite as nice as the SA towels.
So that I could spend the remaining years fo my life sometimes using decent hand towels, I obtained the secret hand towel formula from SA. Here is how they do it (this could be a draft S.O.P. for the rest of the airlines).

1. The plush cotton towel weighs 21g dry and 55 grams wet.
2. It is 12 inches by 9 inches and has the SA logo in the top left corner (see picture)
3. The required amount of water is added to the towels.
4. The towels are microwaved to reach a temerature of not more than 50C
5. Before distribution, the temperature of the towels is tested with the back of the hand to make sure they are safe to use.

The sad thing is that Qantas staff probably never fly on other airlines, or apparently have no way of providing input into the proceedures they use every day. The low quality hand towels have persisted for several years already so maybe they can try to match the world best. I have other suggestions for Australian travel industry which I will put here from time to time under "Travel Log" subheadings. Watch out for next week's entry which will be "Security".

On the Anniversary of Darwin's Book - More thoughts on his illness

It is 1:15 am in Perth, but only 6:15 London Summer Time so I can still say this entry is on the 150th anniversary of Darwin's book "The Origin of Species". I have been too busy to spend a lot of time researching Darwin's illness but it is very easy to conclude that he had a gastric illness by searching the Darwin on-line archives located here. If one searches for "stomach" or "my stomach" you can find about 70 instances where he refers to his illness. If one searches for "heart", "my heart", "palpitations", "pulse" etc. you can find only a few references and most are to do with his normal emotions rather than his physical organic cardiac symptoms. Thus it seems to me that the idea of a cardiac illness is rather over-rated (notably some kind of sympathetic or parasympathetic disturbance caused by chronic Chagas' disease).
However I do concede that Darwin refers often to "flatulance" but rarely if ever to disturbances of the bowels e.g. diarrhoea. Thus it seems that his flatulance symptoms are actually a feeling of distension in the episgatrium which are commonly related to and releived by aerophagia (swallowing air) and eructation (burping) respectively. This type of symptom is common in acidic conditions such as duodenal ulcer and is especially so when accompanied by hiatus hernia and gastro-oesophageal reflux disease (GERD/GORD). But the nausea and vomiting he often suffered from makes gastritis and duodenal ulcer a likely associated cause.
Flatulence can also be due to lactose intolerance and this has been invoked to explain his illness by several authors. This year, Mike Dixon finished a book (Darwin in Ilkly by Mike Dixon and Gregory Radick) where lactase deficiency is championed (I have not read the book yet so cannot give an opinion on the evidence). If Darwin did have milk intolerance then it seems to me that he would have worked out himself that he was lactose intolerant e.g. drink milk = abdominal gas and +- diarrhoea and farting with a lead time of an hour or two. It is interesting to speculate that if lactose intolerance is genetic, then it could be diagnosed on his remains at some future date.
Getting back to my ulcer/Helicobacter hypothesis now, I have previously noted that he took bismuth and various antacids at the hight of his illness. Also, when he was especially unwell, his father prescribed "calomel", which is mercury, yet another heavy metal. At other times he took arsenic. Of course everyone took these things in the early 19th century because there weren't any other antimicrobials. But each of these heavy metals might have been expected to kill H.pylori in the stomach and cause a remission if taken daily for 2-4 weeks.
So, I admit that I am curious about the language Darwin used and the meaning of his "flatulance". I have several secret strategies for finding this out. If it was colonic anal rectal expulsion of air then the case for a carbohydrate malabsorption (lactose intolerance) is strengthened. This could be correlated with a diary of his illness to see if milky foods could correlate with his apparent gassy problems.
Once more I have not discussed psychosomatic causes of his symptoms - there does not seem to be any need to invoke this.
By the way, there is quite a nice new book out by John Van Wyhe which contains facsimiles of some original Darwin research notes in little pockets on the pages. Nice work John. My clock just struck 2 am - time to go.

Fingerprints and Infectious Diseases (e.g. Swine flu)

After I discussed the issue of fingerprints and 'flu virus transfer with a few people in London, I was told this story about the 2000 Olympics in Sydney.
Apparently, they were planning to use fingerprint readers for I.D. at the athletes' access gates but the French medical team objected because the print readers might transfer some diseases and infect their healthy team (which presumably had been quarantined before the events). So lanyards and bar-coded I.D. cards were used.
So in 2000, it was already known that fingerprinting devices were a health hazard!
Well, too late now. The horse has bolted.