Author Archives: Doctor Tungsten
For those of you who want a Tungsten-hard body like Dr Tungsten here’s some handy tips from Stepcase Lifehack.
Step 7 is the hardest, Morpheus a mighty foe.
Tip #1: Be Alert For Opportunities All Day Long
Focus on becoming stronger because there are myriad opportunities throughout the day to strengthen your body. As simple an effort as walking up the stairs to the third floor, rather than taking an elevator, will eventually produce a noticeable effect. Yes, weights lifting, exercise machines and structured sessions are powerful – but so are simple activities carried out every day.
Tip #2: Rest Is Just As Important As Exercise
Make certain you value and allow rest and recovery time. Many believe that if an intense workout feels good and will build muscle quickly, then the smart thing to do is to exercise even more. Muscle builds when exercise tears the muscle down, because it recovers as newer, stronger muscle. Without that recovery time, your muscles absolutely cannot increase in size or strength. Beginners usually start with three workouts per week and the duration and frequency can increase as they grow in strength and power but your body will respond more quickly and more dramatically if allowed to rest during strenuous activities.
Tip #3: What’s “Best” Is What You Will Persist In Doing
There is a constant and ongoing war among fitness experts about whether free weights or weight machines are superior. As far as you are concerned, whatever works best for you is the right choice. If you love competing with the weights on a machine then by all means choose that option. If you despise machines, but eagerly grab that set of dumbbells, then go for it. There is no point whatsoever in choosing exercises that you hate and won’t stick with, no matter what the ‘experts’ say.
Tip #4: You Didn’t Arrive At Your Current Condition Overnight
If you’re flabby and overweight – in other words, totally dissatisfied with the condition of your body – always remember that you didn’t get there overnight. In other words, impatience is a huge mistake. It requires years of neglect and misuse to create problems in your body and it will take some time to repair them. Exercising for a week and then quitting because there are no visible changes is foolish and short sighted. Not only that, but more failure will further erode your confidence and increase the sad condition of your body. You can drastically shorten the time it takes to achieve superb conditioning by using wisdom and discipline but you won’t see changes by 5PM on the first day.
Tip #5: “Compound” Exercises Are More Efficient
Consider that “compound” exercises will get results faster than those exercises that use only one muscle or one muscle group at a time. Yes, your abs may be a disgrace but focusing only on an ab machine won’t pay the dividends of full body exercises. And always remember that exercises which work multiple muscle groups will build fitness much faster – and that’s what we all want, isn’t it?
Tip #6: Don’t Exercise Mindlessly
Don’t exercise of mindlessly. If you pay close attention to your muscles and your body while working out, your results will be much more powerful. On the surface, that doesn’t seem to make sense. But famous, skilled athletes and bodybuilders have stated time and again that they can literally direct their muscles as they see fit.
Tip #7: Natural Sleep = Health and A Fit Body
Get as much ‘natural’ sleep as possible, meaning that drugs and sleeping pills interfere with the natural repair of the body that occurs every night. When we sleep, growth hormone, or HGH. is released into our bodies. HGH stimulates healthy growth, cell repair and the regeneration which is necessary for muscle development. Growth hormone is naturally produced by the body and many athletic scandals have occurred because athletes were building their bodies with the use of artificial HGH. Synthetic growth hormone, even when legal and prescribed by a doctor, can have dangerous side effects. You want to maximize your production naturally and this is done while we’re asleep.
Tip #8: Pepperoni Pizza Is NOT The Perfect Diet Food (Sorry!)
The perfect diet for an athlete or body builder centers around proteins, certain fats that include essential fatty acids (EFAs) and complex carbohydrates like vegetables, fruits and whole grains. Most fitness experts recommend eating multiple small meals rather than three larger ones. This keeps the metabolism working constantly and is less likely to result in fat or overweight.
Tip #9: Water, Water and More Water
Drink lots and lots of water. Water keeps your muscles hydrated which makes them work more efficiently and helps them recover more rapidly. It’s important to know that soft drinks, tea and coffee generally dehydrate the body so don’t assume they are helping your muscles. They’re not.
Superlative fitness requires self-discipline and long term dedication to your goal. Anyone who is going to make this kind of serious commitment naturally wants to reach their goal as quickly as possible and to do this we must be efficient. Following these rules will speed you to your ideal body as quickly as possible.
BOOZE IS GOOD FOR ME!
See, I don’t have a problem, I am moderating the deficiencies caused by the more sedentary lifestyle of a writer/programmer/scientist.
ScienceDaily: Latest Science News
Now I’m off to have another bottle of medicine!
This explains so much about my life. Seriously I’m going to have to get a cooled helmet to sleep in if this keeps up. The Space Jockey?
That’s me in ten years!
There’s a lovely scientific history of Female Ejaculation over at Scientific American.
1) Yes it’s real.
2) No, it’s not urine.
3) Yes, it’s hard to replicate under sterile laboratory conditions for some odd reason.
And on a person note, yes it’s very surprising to get a face full if you aren’t expecting it.
Now it’s time to get to work on part two of this research, which I’ve titled “Doctor Tungsten and the all Lesbian Bukake Brigade.”
We’ve all been there, you’re sitting around working on your latest Doomsday Device and you hit the wall. So what can you do to spark that creativity you need to SHOW THEM ALL? How about have a laugh?
Figure 1: Maybe not quite like this…
via South Park
No, really. Karuna Subramaniam, formerly of Northwestern University, and her colleagues discovered that by improving the mood of their volunteers they could increase the likelyhoood that the individual will have an “aha!” moment while trying to solve a puzzle. Read more here (http://www.scientificamerican.com/article.cfm?id=laughter-leads-to-insight)
And for more on the health benefits of laugher: (http://www.helpguide.org/life/humor_laughter_health.htm)
U.S. Measles Cases Hit 15 Year High
Things you should probably know about measles:
- Measles is one of the leading causes of death among young children even though a safe and cost-effective vaccine is available.
- In 2008, there were 164 000 measles deaths globally – nearly 450 deaths every day or 18 deaths every hour.
- More than 95% of measles deaths occur in low-income countries with weak health infrastructures.
- Measles vaccination resulted in a 78% drop in measles deaths between 2000 and 2008 worldwide.
- In 2008, about 83% of the world’s children received one dose of measles vaccine by their first birthday through routine health services – up from 72% in 2000.
- The average number of U.S. measles cases each year for the past decade has been 56.
- So far this year there have been 118 cases of measles reported in the United States.
Wait…what was that last one? That’s makes this this the worst measles season since 1996. If the average number of U.S. measles cases each year was only 56, which means cases have more than doubled.
What could be causing this you ask? A new-super measles strain? Alien invaders? Global Climate Change? Jenny McCarthy?
Figure 1: Those are the guns she murders your children with.
Yeah, it’s sad when “alien invaders” would make more sense than the reality isn’t it?
Prior to this, most of the case of measles in the U.S. were imported, because we’ve spent over half a century using vaccination to eliminate measles as an everyday infection, but some people seem to want to change that.
So, let’s break that down a bit. Of these 118 cases:
- 40% were hospitalized
- 9 had pneumonia, though luckily none died.
- 105 of them had not been vaccinated.
- 45 of them were between 1-19 years old.
- 39 of the 45 age 1-19 were unvaccinated.
- 24 of those cases were because parents claimed a religious or personal exemption.
So that gives us ~100 preventable cases of a potentially fatal disease, assuming at least a few of these cases were individuals who can’t be vaccinated due to allergies or other biological concerns. Of those, 24 were children and teenagers who could easily have died. Remember folks, measles is the most infectious disease known and in 2009 alone, an estimated 164,000 people died from measles.
Man, that’s a lot of dead people from an easily preventable disease, isn’t it? Of course most of those deaths take place in poor countries where vaccination has proven difficult and expensive, though we are working on that.
So what is the argument for not vaccinating your children?
Figure 2: Admittedly, that’s a pretty good argument from where I’m standing.
This all started out because a guy named Wakefield published a study linking the vaccine and Autism (better dead than autistic, I suppose?). Of course, further research has shown no link between these beyond the fact that autism symptoms often become obvious around the same age vaccines are given in the United States. However, as discussed above: lack of vaccination has serious consequences. For those who don’t like children all that much, this could represent a significant financial burden on the country as well.
So now that everyone knows that vaccines don’t cause autism everything should be okay right? We should throw a party!
Figure 3: Not what I meant.
Well, I guess these guys aren’t that bad. I mean people have been throwing chicken pox parties to immunize kids while their young, that’s worked out okay right? I mean sure, there is a chickenpox vaccine too, but why should we use that?
Chickenpox believed to be responsible for 1/3 of all childhood strokes.
Inflammation of the brain can occur in immune-compromised individuals.
Necrotizing fasciitis is also a rare complication.
And if you happen to be pregnant….
You know what? I think I’m really sold with the Necrotizing fasciitis.
Doctor: “You can take this vaccine, or you can let nature take its course.”
Me: “Well, I’m an all-natural kind of guy, what’s the worst that can happen? ”
Doctor: “Flesh eating bacteria will eat your flesh.”
Me: “So about that vaccine….”
Of course, I know I’m preaching to the choir here. Anyone who is reading my science blog probably already knows that vaccines don’t cause autism, or they’re in my basement tied to a chair with their eyes wired open and being re-educated
What can I say? Don’t allow ignorance and misinformation to run rampant, every article mentioned above is another arrow in your quiver: fire straight and true.
This paper presents a new method for detecting and masking repetitive homologous sequences. The design of TANTAN was inspired by the strand slippage mechanism that generates simple repeats. With the assumption that the slippage events occurred with different offsets in mind, they designed an algorithm that integrates self-similarity at different offsets. This was incorporated into a single model along with posterior decoding, which should allow the algorithm to distinguish background from non-background probability. This method is said to enable reliable homology search for protein–protein, protein–DNA and DNA–DNA comparisons, even for extremely AT-rich DNA.
To test the reliability of TANTAN, they have done a series of comparison to other commonly used methods, including Tandem Repeat Finder (TRF) and DustMasker and SegMasker. Tandem Repeat Finder is unique here in that it uses smaller repeat sequences as seeds to develop consensus sequences, which are then matched with similar sequences in the genome . DustMasker and SegMasker are included as part of the BLAST+ package, and are used to mask nucleotide and protein sequences respectively [2-3].
The standard method of comparison used is to align two genomes and compare the number of alignments to the value expected for random sequence data (evalue). These genomes may be individually or both masked by one of the programs being compared. The initial results shown in Figure 4 of the paper seem to show an extremely high number of alignments following masking by DustMasker, SegMasker and TRF. Figure 5 shows similar alignments, but using TANTAN as the masking program. Here, the alignments are much closer to the evalue than before, and in many cases the number of alignments is less than you would expect from random sequence data. Figure 6 shows the effect of different r values on the percent of sequences masked, where anything above a 0.02 seems unreasonably high. Figure 7 shows the number of alignments with TANTAN used to mask the sequences at different points during the alignment process, where masking the genome at nucleotide level and then converting to amino acid sequences shows a particularly high number of alignments. Lastly, Figure 8 shows the result of a soft-mask, where a mask is applied during earlier stages of the sequence comparison but not later stages, which demonstrates a much higher number of alignments than the similar hard masking shown in Figure 5. The author’s final conclusion is that TANTAN is much more adapt at masking simple repeats than the tested software.
The program is designed to help with the comparison of homologous structures between species; however, there seem to be a number of factors that they don’t take into account. The most obvious of these is that nowhere do they factor in transposable elements(TEs), which may comprise a significant portion of the genome. For example, 45% of the human genome, 55% of the opossum genome, and 73% of the maize genome are composed to TEs [4-6]. They state “since sequences do not evolve by reversal, there are no true homologs in these tests” during the testing stages, but many transposable elements can insert in both forward and reverse orientation . This makes it likely that many of their “spurious similarities” were in fact informative insertion sites, and may explain some of the high number of alignments seen in the theoretically random data seen when testing the plant and animal genomes. To compound this error, there never seems to be a point where the so called spurious sites were collected and compared at a sequence level to check for any actual homology.
In addition, there doesn’t seem to be any direct comparison between the sequences that make up the different ranges of masking. In Figure 6 we see a wide range of different numbers based on the different r values used, but there is no indication of what is actually being masked beyond the baseline of 0.005. Obviously in the heavily AT-rich genomes you are getting a lot of false positives which are accounted for in TANTAN, but what about the other genomes? Is TANTAN masking genomic features similar to simple repeats, or is it become at that level we’re seeing transposon masking, or is it masking random nucleotides that bear some vague repetition. Their protein – protein alignment testing seems to be a bit more grounded, since protein sequences will be more conserved, but TANTAN doesn’t seem to handle translated sequences very well as seen in figure 7.
Overall, the paper seems to be lacking in practical testing. TANTAN lacks RepeatMasker’s convenient masked region only file output, which would have made digging through the actual data much easier. Too many bioinformatists treat this kind of graphs and statistical analysis as gospel or black boxes that you never look into. The test design here is very clever, but it seems like understanding of the genomic landscape of different taxa was a bit deficient. The paper should have focused on TANTAN’s specific strengths in comparison to other available programs, rather than comparing with a set of somewhat ill-suited comparisons. The lack of a RepeatMasker comparison is particularly jarring, since I believe it would be the go-to program for masking large portions of the genome for homologous analysis. It should also be pointed out that the scoring system use and the variables set made a large difference in the quality of the output in TANTAN, and while a previous paper covers similar ground with the other programs, I feel that a direct comparison of the “optimized” output for each program would have been more valuable. I also feel a figure comparing a genome masked with TANTAN and a genome masked with another program to both genomes masked with TANTAN and both genomes masked with the other program would be useful; the difference in the range used for the Y-axis in Figure 4 and Figure 5 seems designed to make the number of alignments seem excessively high in the other programs. The other programs within the paper possess other functions that TANTAN doesn’t perform, the usefulness of TRF in TE identification being of particular note.
TANTAN’s primary strength seems to be its ability to perform simple repeat masking in AT-rich genomes. It does an admirable job in masking the simple repeats and should be comparable to the other programs used for de novo masking and the computational resources used should make it available to a causal desktop user for most genomes. However, as mentioned in the paper, the hand optimized parameters will likely make it poorly suited for “right out the door” use.
As mentioned above, there is no “only repeats” output to provide easy access to the masked sections for analysis. This makes TANTAN particularly ill-suited for the study of repeats, especially when compared to other programs such as RepeatMasker or TRF. There is always the possibility of extracting the masked areas using another program, which wouldn’t necessarily be computationally difficult, but it’s an extra step which should be unnecessary. However, the algorithm itself seems to be well designed, and is probably better suited to be implemented as part of a larger framework or more specifically specialized tools. While functionally the same, a frontend with commonly used parameter combinations designed to work best in a given set of circumstances would make the program much more available to the casual user.
- Benson,G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res., 27, 573–580.
- Morgulis,A., Gertz,E.M., Scha¨ ffer,A.A. and Agarwala,R. (2006) A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J. Comput. Biol., 13, 1028–1040.
- Wootton,J.C. and Federhen,S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol., 266, 554–571.
- Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409:860-921
- Mikkelsen, T.S., B. Aken, C.T. Amemiya, J.L. Chang, S. Duke, M. Garber, A.J. Gentles, L. Goodstadt, A. Heger, J. Jurka, M. Kamal, E. Mauceli, S.M.J. Searle, T. Sharpe, M.L. Baker, M.A. Batzer, P.V. Benos, K. Belov, M. Clamp, A. Cook, J. Cuff, R. Das, J.E. Deakin, M. Grabherr, J.M. Greally, W. Gu, R.L. Jirtle, S. Mahony, M.A. Marra, R.D. Miller, R.D. Nicholls, A.T. Papenfuss, Z.E. Parra, D.D. Pollock, D.A. Ray, J.E. Schein, T.P. Speed, J.L. VandeBerg, M.J. Wakefield, C.M. Wade, J.A. Walker, C. Webber, J.R. Weidman, X. Xie, M.C. Zody, Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, J.A. Marshall Graves, C.P. Ponting, M. Breen, P.B. Samollow, E.S. Lander, K. Lindblad-Toh (2007) Genome of the marsupial Monodelphis domestica reveals lineage-specific innovation in coding and non-coding sequences. Nature 447(7141):115-230.
- Meyers, B.C., Tingey, S.V., and Morgante, M. (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Research, 11:1660-1676
- Sela et al (2010): The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates. Genome Biology, 11:R59