Check out this summary of results on aging in nematodes. The layman’s summary is this:
Aging is thought to be due to accumulated damage. As we age our bodies get lots of microscopic injuries and accumulated cellular damage. Over time it adds up and our bodies break down and we die. This is the prevailing hypothsis because it’s easy to see the mechanism for how it came to evolve.
An alternate hypothesis is that our genes dictate that we age and die, and it’s programmed into us. So rather than breaking down, aging is the result of changes in metabolic regulation.
This study finds evidence supporting the latter model, which is pretty interesting. To summarize their experiment they used gene-chips to exhaustively search for genes that change their expression level in old worms, and linked many of them to a single regulatory protein (transcription factor). Then they tried to put stresses on young worms to see if they could increase the level of this transcription factor, effectively making the worm age faster. They were not able to, which indicates that the transcription factor levels are not a function of stress. Of course, this is only true if they were using the “right” stresses on the worms.
In any case, I’m always excited to see work done that supports any sort of programmed-senescence model, because it points toward the possibility of regulating aging by only tweaking a few things.
A group of oceanographic scientists are in the process of publishing results indicating that the ocean has stripes. They used successive levels of data filtering to remove large scale variations like currents and waves and temperature gradients, and they were left with these bands of very small variation in temperature and velocity.
An interesting observation here is that they repeated their approach on the output from a Japanese computer running the “Earth Simulator” and found very similar stripes in the output from that model.
Maybe I’m just overly skeptical, but it seems to me that if you run a bunch of data filtering and end up with a bunch of surprisingly fine-scale features you have to wonder if it’s an artifact of the analysis. And the fact that they found the same features in the model output, when presumably the model wasn’t programmed to have this behavior, seems to indicate that the stripes are coming from the data filtering and are not real phenomena. Otherwise that seems to say that the Earth Simulator model is so accurate that it was predicting previously unimagined phenomena in the ocean, which would be pretty remarkable in itself.
For the record: I’m not an expert in oceanography, I’ve just got some experience modeling physical systems. They may be right, and there may be tons of stripes overlaid on the ocean. I’m sure their first thought was that it was an artifact, and it must have checked out after reviewing the analysis. It just seems a little fishy.
I came across this in summary for at Ars.
Andy Grove, the famous CEO of Intel, has spoken out publicly against the pharmaceutical industry. I’d like to comment on a few of his statements.
First a few words on my perspective. Before moving to biotech I actually had a stint in process development at Intel, so I’m pretty familiar with the industry and the technology. Now I’m in R&D in the biotech industry which, while not really the same as pharma in general, still gives me a good perspective on the challenges of drug development.
Mr. Grove is a very smart guy who’s been very successful in his industry. He’s not just a management-focused CEO, but an actual technical expert who’s made it to the top. My point here is just that he’s got a credible reputation for technical matters.
I picked the semiconductor industry because it’s the one I know; I spent 40 years in it, during which it became the foundation for all of electronics. It has done a bunch of unbelievable things, powering computers of increasing power and speed. But in the treatment of Parkinson’s, we have gone from levodopa to levodopa. ALS [Lou Gehrig's disease] has no good treatment; Alzheimer’s has none.
This is, unfortunately, a nonsensical comparison. Grove’s main point is that the semiconductor industry has made huge strides in 40 years but the pharma industry has not.
Continue reading ‘Andy Grove is mistaken about the drug industry’
You may have seen the stories going around the net today about a scientist who’s discovered how to burn salt water, and that the DOE is going to investigate this as an alternative source of energy. Let me explain why this is stupid.
Dr. Roy said the salt water isn’t burning per se, despite appearances. The radio frequency actually weakens bonds holding together the constituents of salt water — sodium chloride, hydrogen and oxygen — and releases the hydrogen, which, once ignited, burns continuously when exposed to the RF energy field. Mr. Kanzius said an independent source measured the flame’s temperature, which exceeds 3,000 degrees Fahrenheit, reflecting an enormous energy output.
Let me break this down for you, serious science style:
Continue reading ‘Burning salt water will not fuel your car’
I’ve been involved in a few discussions recently about stem cell research, and I think there’s a lot of misunderstanding, in addition to outright deception, going on in the public debates.
By way of introduction, I’m a Ph.D. researcher at a biotech drug company and I’ve been involved in research in academia as well. While I am involved in bacterial / mammalian cell fermentation, and not stem cells, I have a good understanding of this issue, and the technologies involved. It’s another example of attempts to politicize science, and politicize facts. The science says embryonic stem cells are the way to go. Period. End of story. If you think there’s a morally unjustifiable cost associate with those benefits then just say that. That’s an intellectually honest debate to have, and one that could be had in the public sphere.
Continue reading ‘Stem Cell Research’
Clinical trials are the statistical testing of new drug molecules in human patients to determine safety and effectiveness. You frequently hear about drugs having “promising results after Phase II clinical trials” and you may not know exactly what that means.
First, to be clear, a great deal of development effort goes into a candidate molecule before it ever enters a person. There will have been extensive lab tests, tests in animal models (an animal, such as a rat, which has a condition that mimics the human disease of interest) as well as toxicity tests in animals. In general, perhaps 1 in 1000 molecules makes it all the way to phase 1 trials. In biotech, the ratio is probably higher, but that should give you an idea. And once you enter into clinical trials, the majority (perhaps the great majority) of candidate drugs fail at each phase.
A quick summary is:
- Phase I – is it safe?
- Phase II – does it work?
- Phase III – fully, statistically define the drug
Continue reading ‘What are clinical trials?’
I came across a short piece in the New York Times recently that’s worth pointing out. It’s about a particular startup in the Bay Area that’s focused on using metabolic engineering to produce anti-malarial drugs and the next item on their agenda is fuel.
For the layperson, metabolic engineering is a step beyond genetic engineering. Metabolic engineering involves creating a new network of complementary reaction pathways within a cell, essentially creating whole new ways of making biological products. In a big picture sense, metabolic engineering treats the cell as a factory, and adds or optimizes structures within the cell for some design purpose.
Continue reading ‘Metabolic engineering as path to medicine and energy’
I’m a researcher in a pharmaceutical biotechnology company, and I’m concerned by the lack of public understanding about what it is we do. In this article I’ll explain some of the process of pharmaceutical manufacture at a biotechnology company, and how you go from a cell stored in liquid nitrogen to a vial of drug for injection. This is intended to be a readable, layman’s explanation of the process. My perspective is fermentation-centric, so apologies to the areas I can’t fully represent. In a later article I’ll discuss more of the research process, where I am involved. I’m also going to sprinkle the article with links to references that have more detail and explanations of technology or equipment.
The master cell bank
The basic concept in biotech is that you identify a molecule that you want, and the sequence of DNA that could be used to produce that molecule. Then you genetically engineer a cell line (CHO or E. coli) to produce it and come up with the correct bioreactor conditions so that they can grow and produce it. Once you have settled on this combination of cell and DNA you place that “master” cell line in liquid nitrogen for permanent storage. This is your gold standard copy from which all drug production starts. You probably have more than one master cell bank to protect you from things like fire and earthquake, since if you lose the master cell line you will have no FDA certified source of cells to produce your product! That would be bad.
The first step in production is to take some of your master cell bank and carefully grow it up in a bioreactor. The goal here is not to make any product, but just to make some more cells, which can then be frozen as a “working cell bank.” Because the master cell bank is so important you try to avoid accessing it as much as possible. Every now and then you take some master cells and create a new working stock.
Continue reading ‘How biotech drugs are produced’
Papers is another “iTunes for PDFs” program, only it seems to be dripping with 10.4 programming magic. It’s aimed at mac using researchers (and the pre-release features are geared toward PubMed users), so the general audience won’t care, but for a small subset of people it’s really fantastic.
I think this thing incredible, but I’ll go ahead and start with the caveats:
- It’s a “preview release,” which means it’s far from done.
- It crashes periodically.
- The preference pane is completely empty.
- It only supports PubMed right now (but has a plugin architecture which will eventually allow for many search engines).
Now, even given the above, I still plan on using it as my main journal article program because it gets so much else so right.
Continue reading ‘Papers – iTunes for research articles’