24 carat gold test tubes

Perhaps a more inert material should be used for test tubes. As we've discussed before chemicals leaching from test tubes can lead to enzyme inhibition. It has also been demonstrated that plastics can interfere with results in cell culture and even more recently it has been shown that plastics can affect protein and DNA measurements by UV absorption measurements, by as much as 300%.

Cloning Perfection

10/10 positive clones. Not the first time, but each is just as sweet as the last. And a sexy gel to boot. What can I say? When you're hot, you're hot.

Junk DNA and Transposon Driven Evolution

A press release out of the Genome Institute of Singapore is claiming a function for junk DNA. The researchers show that a number of transcription factors bind repeats found in transposable elements.

More than 50 percent of human DNA has been referred to as "junk" because it consists of copies of nearly identical sequences. A major source of these repeats is internal viruses that have inserted themselves throughout the genome at various times during mammalian evolution. [...] The researchers showed that from 18 to 33% of the binding sites of five key transcription factors with important roles in cancer and stem cell biology are embedded in distinctive repeat families.

Now I could be wrong, but I thought we already knew that portions of these transposable elements acted as transcription factor binding sites (for example see here) so I don't think Larry over at Sandwalk is going to have to revise his estimates of junk DNA percentage yet. But what about the "deflated ego problem"? Is this an answer to Larry's excuse #5: that humans are more complex than other organisms in spite of similar gene numbers because of more complex regulatory mechanisms? Unfortunately I don't have access to the paper, but the press release and abstract seem to think so.

Over evolutionary time, these repeats were dispersed within different species, creating new regulatory sites throughout these genomes. Thus, the set of genes controlled by these transcription factors is likely to significantly differ from species to species and may be a major driver for evolution.

The argument here isn't for more complex gene regulation in humans, but rather different regulation depending on where these elements landed in early evolutionary history.

Quack of the Week: Toby Alexander and DNA Activation

According to dnaperfection.com:
"What exactly is DNA Activation?
Most people know that DNA is the 'blueprint of life' and is located in every cell of the body. In addition to each chromosome's 2 strand double helix of DNA, there are an additional 10 etheric strands of DNA available to each human, which have been dormant since the beginning of recorded history. Each additional strand possesses attributes that permit the individual to perform greater human accomplishments. Scientists acknowledge that we currently only use 3% of our current 2 strand DNA. Thus we live in a society where people are sick, unhappy, stressed out, create wars, have difficulty experiencing love, and are totally disconnected with the universe. Most people have to meditate for many years just to have a so-called 'mystical' experience, that's how disconnected we are now. Imagine activating 100% of your 2 strand DNA, PLUS 10 additional strands! You will go from using 10% of your brain to becoming a multi-dimensional being with psychic, telepathic, and manifestation abilities beyond anything you've ever dreamed of. Plus, you will stop the aging process and actually start to rejuvenate to look and feel YOUNGER. This is the Original Divine Blueprint, what man USED to be. It has been written that Jesus had 12 strands of DNA activated. There have been children born throughout the history of humanity to raise the frequency of the planet that have more than 2 strands of DNA active - they are known as Indigo children. These are the incredibly intelligent, loving, and amazing children that are being mistakenly diagnosed as having A.D.D. because they are too smart to pay attention in class. Your DNA is your blueprint of life and is what controls every single function inside each of your cells. If you change your DNA, you really will change your life."

This has got be one of the most blatant corruptions of molecular biology I have ever seen I my entire life. Check out the rest of the site at dnaperfection.com for some more laughs. The material is endless - I can't even begin to cover it all here. These guys are TOTAL lunatics.

Found on the Tokyo subway

The caption reads: "based on the natural ingredient formulation, collagen plays an essential role to your body". I had a chuckle. I'll try to see if I can bring back a bottle of natural DNA collagen...

UPDATE- "Anonymous Coward found a poster on the Tokyo subway advertising Natural DNA Collagen, a health drink. I found it for sale at Rakuten - about $300 USD for four 720 ml bottles. What a bargain! Ingredients: Collagen, Vitamin C, Vitamin B1, Vitamin B2, Vitamin B6, Vitamin B12, Hyaloronic Acid, Chondroitin Acid, Zinc, Salmon Sperm. This last ingredient must be where the DNA comes from…."

Scientists, Arm Yourselves Against DNA Denialism!

These days it seems that anyone who questions a widely held scientific belief is a delusional "denialist". Are you considering suggesting the hypothesis that global climate change is driven primarily by cosmic radiation rather than human activity? Don't bother. Everyone knows global-warming deniers are in cahoots with big oil. Pondering whether public health and education measures might be more effective than anti-retroviral drugs in combating AIDS in South Africa, or asking exactly how HIV infection eliminates CD4 T cells? Shut the !@#$% and get back on the band-wagon already you HIV-AIDS denialist! You've obviously been brainwashed by the LSD you got from some burnt-out, pot-smoking scientist from California, like Peter Duesberg or Kary Mullis. Have you ever dared to question the prevailing deterministic model of stem cell division? Stem cell denialist! Every day you spread doubt is another day a person with ageing cells will have to go without replacements. Or worst of all, has it occurred to you that all available molecular phylogenetics data does not fit into the "universal tree of life"? Ha! Did God tell you that on a mountaintop, you evolution-denying, modern-day Moses? I hope you burn in hell!

With all the rampant denialism going on out there, we smarty-pants scientists need to prepare for the next outbreak. The question is, which form of denialism will be the next to hit? I think it only makes sense that those conniving little bastards will go after the very foundations of modern genetics and molecular biology - the "theory" that the genes encoding our biological traits are contained in cellular deoxyribonucleic acid (aka "DNA").

So how to prepare? I propose a new tactic. No more bloody and violent exchanges of capital letters and exclamation marks on the battle fields of the blogosphere. Enough with the "YOU ARE A DENIALIST BECAUSE YOU ARE DUMB AND IRRATIONAL AND WILL NEVER ACCEPT REALITY!". No more "it's in a peer-reviewed journal and has been regurgitated by a lot of other peer-reviewed journals so it must be true". No more "this is not even really a debate amongst REAL scientists, so I don't have to bother to explain it to you". No more "I did a PubMed search on your hypothesis, no hits came up, so you're wrong!!!". No more "I hold a BSc, an MSc and a PhD from Oxford, Cambridge and Hogwarts, whilst you barely satisfied the conditions of your community college, ergo I am clearly in the right and you, sadly, are mistaken".

Yes, I would like to propose a radical new approach in the war on denialism. I call it "explaining science". This means doing nothing except explaining experiments and their results. (aka "the evidence"). When people are unconvinced or do not immediately understand, we rephrase and try again. And again. And again. They still don't get it? Maybe we draw a picture. A cartoon. Maybe an animation. Maybe a bulleted list. Maybe use statistics, a pie-chart or a bar graph. Make a video, a hologram or a video-game. Do an interpretative dance. Whatever it takes. Just don't call them denialists, or you'll remind them they're supposed to be denying something (shhhhhhh). And maybe, in the end, we will convert the denial-lovers to science-lovers. Or perhaps some will resist and forever remain beyond our reach. Maybe the disease of denialism is incurable or even genetically encoded in an unlucky few defectives. But I'll be damned if we don't die trying!

So, to prepare for the eminent strike against DNA, all we have to do is remember how we know that DNA is the genetic material. Keeping the experimental evidence at our fingertips, we will be well-armed to defend science from the denialists. What? Can't remember why? Don't worry, me neither. Hey I'm just a graduate student in biochemistry after all. Luckily, Larry Moran, a real scientist who's old enough to still remember the evidence and knows how to blog, points to the experiment in question (that's why they call him 'Professor'). It was Canadian Oswald Avery's 1944 paper which showed that DNA, but not RNA, carbohydrate or protein could transfer the genetically transmitted trait of virulence from bacterium to another. You can read commentary in science blogger John Dennehy's "Citation Classic of the Week". Even better, check out this awesome Cold Spring Harbor animation describing the experiment. No denialist can withstand the power of animations!

So, fellow scientists, be vigilant for the emergence of the DNA denialists when they strike. Know the enemy, but more importantly, know the evidence!

(PS- This was a humor piece, whether you find it funny or not. Except the part about the Avery paper. So don't be sending me any hate-mail.)

1010 by 2010

That's 10¹⁰ base pairs of DNA sequenced or synthesized by one person in a single day. That's a hell of a lot. More than enough to cover the whole human genome several times. And that's just one person. Imagine how much a factory full of monkey could do. If you think this sounds ridiculous, read the rationale for the prediction in this great article. As shown below, the projection is based on the current exponential growth of biotechnology, mimicking the trend known as Moore's law, where the number of transistors that can be fit on a microchip has been growing exponentially for the last 50-60 years. The article makes some interesting comparisons between the two industries and also features some of the best discussion I've read on the future of biotechnology and its place in society.