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Comment: Re:So there's 100 or so unimmunized? (Score 2) 387

by Bowling Moses (#47240983) Attached to: California Whooping Cough Cases "an Epidemic"
From your link: "cowpox bears no analogy to smallpox." Cowpox and smallpox viruses are very similar, assigned to the same viral genus. We have sequenced the entire genome of each and their close relationship is undeniable. Here's an article for exampleAnalysis of the complete genome of smallpox variola major virus strain Bangladesh-1975. From the abstract: "Most of the virus proteins correspond to proteins in current databases, including 150 proteins that have > 90% identity to major gene products encoded by vaccinia virus, the smallpox vaccine." I'm sure if I spent more than 10 seconds on google I could find a lot more.

Comment: Re:NOW they realize this (Score 1) 126

"The main thing that needs to be reversed is to restore the separation of management and science."

What separation? If as a PhD you can't think up more ideas worth following up than you can do the hands-on work yourself you're a piss poor PhD. This can start at a very junior level: I am no one special but I had three undergraduate research assistants assigned to me as a senior grad student and I was able to train them and still get back more work than I had spent in training and managing, a win-win as all were supporting authors on at least one of my papers and all went on to careers in science and medicine. I don't know of any PhD level scientists who did not have at least one direct report before finishing up their postdoctoral positions (which is roughly the transition from early to mid career in science for PhDs). Now that I'm nearly ten years post-PhD I don't see a change in trend: the more senior you are, the more likely you are to have more numerous and more senior people reporting to you. It's more a continuum than anything, and having spent over 15 years in academia successful professors are top notch grant writers, are completely in charge of science, oversee marketing (if any), are completely in charge of data presentation, and at a bare minimum oversee their subordinates' career development. It's a rare professor that does much bench work, and I've known awesome scientists who still spent an amazing 10 hours a week at the bench and awesome scientists who hadn't spent a single second at the bench in 20 years, though both extremes still had a typical 70 hour work week.

Comment: Re:And this is somehow supposed to be a surprise? (Score 1) 1010

by Bowling Moses (#45824073) Attached to: New Study Shows One-Third of Americans Don't Believe In Evolution
"Is anyone actually surprised by these poll results?"

From the top line that so few Americans are scientifically literate with respect to evolution, no. We're always near the bottom when industrialized nations are ranked by understanding evolution. What surprised and encouraged me is how much better it's getting. The poll broke out the demographics and there is a strong age bias:
age______% believe humans (animals) evolved
65+______49 (50)
50-64_____59 (62)
30-49_____60 (64)
18-29_____68 (73)

Comment: Re:Why reinvent the wheel? (Score 2) 663

by Bowling Moses (#45311605) Attached to: A Math Test That's Rotten To the Common Core
"Teachers who can't teach (even if they know their subject backwards and forwards) should be fired."


"It should be possible for anyone with the proper qualifications to teach whether they have a "teaching certificate" or not; imagine a person retiring from IBM teaching a computer class or a retiree from the financial field teaching economics."

Since they don't have any experience teaching, let alone teaching a class full of people aged 18 and younger, they would probably be horrifically bad teachers.

Comment: Re:Honesty? (Score 2) 440

by Bowling Moses (#44343165) Attached to: How Climate Scientists Parallel Early Atomic Scientists
I'm not a climatologist I'm a biochemist, so I'm not qualified to speak professionally on the subject. Data sets may or may not get thrown out in different disciplines. When I worked in an entomology lab the original data sets weren't kept either, there wasn't room in the freezer and they'd degrade after a while there anyway. In protein x-ray crystallography the diffraction patterns (a series of around about a hundred to a couple hundred very large digital images) quickly get processed and reduced to a couple megabytes (that are deposited and publicly available). The stacks of tapes/CDs/DVDs/whatever of diffraction patterns are held on by the original lab for several years to gather dust, but eventually get lost, thrown out, or are on media that nobody can read anymore. If climatologists are doing something similar I don't see reason for concern.

The claim that there are those "...who will do anything including manipulation of the raw data to further their political goals." is an extremely strong claim, the kind that if proven ends careers in disgrace. I would have to have such a claim very well evidenced before I'd accept it, but haven't heard anything that comes close.

Comment: Re:Honesty? (Score 1) 440

by Bowling Moses (#44342301) Attached to: How Climate Scientists Parallel Early Atomic Scientists
Enzymology and protein structure/function relationships. I like my relative /. anonymity so I won't go into details. I redid the work, attempted to fit his model to the data and it was clear that it didn't work, built a new model that did, and that was also compatible with previously known data from several different areas where his model was not. Nothing special.

Comment: Re:Honesty? (Score 2) 440

by Bowling Moses (#44340151) Attached to: How Climate Scientists Parallel Early Atomic Scientists
80% crap? No. Science papers either generate more questions that are followed up by colleagues and competitors, or are crap nobody is influenced by, nobody cites, and nobody reads. Mistakes get caught--the second paper I wrote as a graduate student tore a well established professor a new asshole over a mistake he had published. I didn't care that I was a nobody and kowtow to the bigshot, I saw a mistake made on what was my thesis project and went for the jugular. I replicated the results, added more data, and aside from minor edits from my advisor I wrote the paper all on my own. I didn't do anything special and I'd expect the average grad student to do the same. We're trained to take the rank of somebody with a grain of salt including all the way up to Nobel laureates. A lab I was in collaborated with one a few years before he earned the prize. We (the grad students and postdocs--the bottom rungs of the scientific ladder) thought of him as somebody who was very bright, very aggressive, and who was almost always right but definitely did not dot the i's and cross the t's. If he made a mistake (rare) or went too far too fast (often) we made a note of it, knowing in our supporting role we'd have to run extra experiments to check it out. None of this is special, it's everyday workaday science from a nobody in the trenches.

Contrast that with an attempt at conspiracy. A nobody, one who's already gotten used to not trusting everything a Nobel laureate or National Academy member says, is going to tease that apparent mistake apart, find another, and another, and then smell blood and scientific glory in equal measures. And that nobody is pretty much everybody in science.

Comment: Re:Umm, this is founded by the us military (Score 4, Informative) 38

by Bowling Moses (#44200541) Attached to: Biologists Program <em>E. Coli</em> To Patrol For Pathogens
The military funds far more than weapons R&D. I've worked on a project to develop insecticides against mosquitoes that was funded by the US military. There are no weapon aspects, it was to protect American troops against diseases (dengue, malaria, etc.) that some species of mosquitoes can spread. The military has funded things that seem off the wall, like marine biology research trying to figure out a why jellyfish light up in the wake of a ship. Naval aviators have found their way back to carriers by following the carrier's fluorescent wake, but the same could be used by an enemy and the Navy wanted a way to make it stop. Didn't work out, but there is some interesting basic research on jellyfish and Green Fluorescent Protein that was produced as a result. The military also funds vaccine and antibiotic research, research into new surgical techniques, prosthetics, renewable energy sources (ie biodiesel), and a lot of other non-weapons research.

Comment: Re:Valid science isn't the only yardstick. (Score 4, Interesting) 134

by Bowling Moses (#44024183) Attached to: Proposed Rule Would Drastically Restrict Chimp Research
"A key part of the problem is that too many of today's researchers are only trained in the techniques that were made elegant 100 years ago and naturally see the increasing use of newer technology as a threat to their way of life."

I do biological research for a living, and have done so for many years, in multiple different fields, in different universities and now in the biotech/pharma industry. No technique I use existed 100 years ago any more than any technique a programmer uses existed 100 years ago. The majority of biochemistry and molecular biology techniques that I use have their primitive origins in the 1960s-1990s, depending on what the technique is, and the overwhelming majority have been heavily modified, adapted, repurposed, and improved since their introduction. Far from being afraid of new technologies and new techniques biologists are absolutely driven to use them, find them, adapt them, and invent them. Who do you think comes up with new techniques, including computer simulations relevant to biological research? People who do biological research of course! There are whole research journals devoted to nothing but new techniques, every one of them invented by some variety of biologist! There are hundreds of biotechnology companies where biologists do little else besides come up with new techniques (yes, including computer simulations and programs) that they can then package and sell to other biologists. Pharmaceutical companies spend many millions of dollars testing new techniques--I've got several different projects assigned to me right now that are nothing but testing and adapting new technologies. A pharmaceutical company that is not constantly innovating goes bankrupt, and a biologist who doesn't innovate is an unemployed and starving biologist.

Comment: Re:Vitamin C... (Score 5, Interesting) 105

by Bowling Moses (#43797831) Attached to: Scientists Find Vitamin C Kills Drug-Resistant Tuberculosis
"Really, this will likely be quickly quashed by the Pharmas. Or they will patent a delivery transport - with the only FDA-approved administration protocol."

Those actions are pretty much diametrically opposed. Option one, quash something that's already known presumably by managing to get a hold of the IP (good luck) and then sitting on it for years using a minimum of effort and cost. Option two, take something that works only on tuberculosis culture, do the R&D to make it work in humans, get it through clinical trials, then manufacture it and try to make a profit. Tuberculosis is a grand master at hide and go seek. It lives inside of human cells part of the time so delivering the vitamin C/vitamin C derivative is non-trivial. Even for a pathogen hanging out nekkid in the bloodstream the delivery of the drug to its target is non-trivial, 10 years and $1 billion of R&D is the rule of thumb to get to FDA approval from early stage research.

Comment: Re:Oh god, please die in a fire right now (Score 1) 227

"I'm sure that there are certain sequences of nucleic acid or protein that, once synthesized and not "contained" could represent an existential threat to life on this planet."

Nope. Nucleic acid is not terribly stable stuff and for relatively short sequences every possible combination already exists in nature. Proteins aren't terrifically stable either and the vast majority require a three dimensional fold on top of the chemical structure in order to function. You can get rid of that fold-denature the protein-by a large number of means. Even if you still have properly folded protein its activity is heavily impacted by temperature, pH, presence of salts, concentration, etc. Life has evolved over billions of years to consume, break down, and reuse nucleic acids and proteins. The risk factor is around that of somebody manipulating water to go all ice-nine on us.

Comment: Re:Betteridge's Law has been beaten (Score 2) 605

by Bowling Moses (#42915675) Attached to: Ask Slashdot: Is the Bar Being Lowered At Universities?
"I think the bar was lowered to soak up all the cash the various levels of government have been dumping into the institutions' coffers. The governments appropriate more money, the schools have to dig up more students to get the bucks."

This is the exact opposite of what has been happening. Public universities have had their budgets repeatedly slashed over the last several decades. A state university used to get about 80% of its total budget from the state. Due to those budget cuts a state university is lucky to have 25%, and some get less than 10%.

Comment: Re:Kuhn Paradigms (Score 1) 265

by Bowling Moses (#42525031) Attached to: Does All of Science Really Move In 'Paradigm Shifts'?
"Discovery of DNA was an utterly world changing event, yet it appeared rather recently."

The history is more complex than that. Friderich Miescher first isolated what he called nuclein (now nucleic acids) from white blood cells in 1869. The work wasn't published until 1871 because the substance was a fundamentally different compound (organic chemistry was still fairly primitive). He did demonstrate that nuclein was from the nucleus and that it contained nitrogen and phosphorus but not sulfur. While he suggested that nuclein might play a role in heredity the thinking of the time was that heredity was too complex for merely one type of molecule to account for it. Albrecht Kossel later received a Nobel for working out much of the chemical structure of nucleic acids, from 1885 to 1901 he isolated and characterized adenine, cytosine, guanine, thymine, and uracil, the bases that make up DNA and RNA. However it wasn't until 1952 that it was shown that DNA rather than protein was the genetic material by the Hershey-Chase experiment. The DNA double helix was described in 1953, that proteins were encoded in triplet codons demonstrated in 1961 and all 64 codons in the "universal" code deciphered by the end of the 1960's. Eventually we come to PCR, exogenous protein expression, genome sequencing, etc. but there are a lot of small steps before we get to the current revolution, which from the point of view of a biologist isn't so revolutionary. To a public (and that includes us biologists at least as far as our non-professional lives are concerned) having to get used to genetically modified crops, human insulin produced by bacteria, the possibility of personal genome sequencing, etc. is fairly large and sudden.

Comment: Re:Not interesting (Score 4, Interesting) 85

by Bowling Moses (#42454259) Attached to: World's Oldest Fossils Found In Australia
”Yes, but things like how DNA and ribosomes work, and the basic molecular machinery would have already been set in stone even in bacteria that old.”

Abiogenesis is thought to have taken place somewhere between 3.9 and 3.5 billion years ago and these traces of life (textures on the surface of sandstone that have altered C12/C13 ratios suggestive of life) are dated 3.49 billion years ago. Calling them bacteria, or even saying that they had DNA and/or ribosomes, may be presumptuous. They’re old enough that conditions of the RNA world hypothesis might still apply. They might not have DNA at all but use RNA (or something else) as genetic material. They might use RNA instead of proteins for catalysis, which could obviate the need for protein-building ribosomes. This life might not be cellular, could just be primitive liposomes that chaotically break and reform, briefly shielding some set of catalytic molecules that when you average them out over a large area—say a cubic millimeter—the whole system is able to keep functioning and making more of itself.

But let’s ignore all of that and say that this stuff, whatever it is, has DNA. Does it only use the four canonical bases or does it use them and/or something else? How good is it at keeping deoxyribonucleic acids from being used alongside ribonucleic acids, or is a mix important in some function(s) at this very early stage? Suppose it does use just the four canonical bases, and just the four (five) bases for RNA, and has ribosomes, and has the central dogma in place of DNA->RNA->protein. What’s the protein like? Is the universal* genetic code in place at this point? Are there just 20 amino acids, the same 20 currently in use, and are they encoded by triplet codons? After all valine, leucine, and isoleucine are pretty much the same as far as protein biochemistry is concerned and usually can substitute for each other with little or no impact, so why have all three? Could there be a different set of amino acids, one that is potentially encoded by pairs of codons or mixed pairs and triplets?

Let’s ignore all of that and say we’ve got life, actual cellular life, that uses DNA with just the four bases, with negligible confusion with RNA, that the mRNA and tRNA and ribosomes are all worked out (and ignoring ongoing evolution), with just the 20 amino acids using the universal* genetic code. Does this organism make its own cellular membrane? There’s a whole bunch of synthesis involved with making the components of a membrane. Does it use cholesterol or other steroids? A modern cell membrane has more than phospholipids. Does it have a cell wall? That’s a completely different set of questions as there are many different cell wall structures and components in modern prokaryotes. What is the energy source for these organisms? Are they heterotrophic? How? Are they photosynthetic? How? Are they sulfur-reducing prokaryotes? How? Are they predatory? Do they secrete chemical compounds that lyse their neighboring prokaryotes? How?

It’s trivially easy to ask questions about basic chemistry, biochemistry, and genetics when it comes to these organisms, assuming of course we would grant them as being alive, when we’re dealing with something from 3.49 billion years ago. I do not necessarily agree with “fine tuning” either since there are geologically short periods of time that witness tremendous changes in life forms. The emergence of aerobic life about 2.5 billion years ago is one such point; oxygen would likely have been poisonous to the life forms in TFA. The emergence of eukaryotes about 1.6-2.1 billion years ago would be another, as would multicellular life appearing shortly afterwards. Throughout all of this the archaea, bacteria, and/or their ancestors would be present, and would be evolving in response to their changing environment.

I happen to have done some work in entomology so I have to mention insect evolution. The Paleozoic period is 541 to about 250 million years ago. The oldest definitive insect fossil is Rhyniognatha hirsti and dates to about 400 million years ago, about the same time that the first terrestrial ecosystems were being formed. Beetles didn’t emerge until 300 million years ago and there are now nearly 400,000 known species. 220 million years ago—well after the Paleozoic—the mosquito and the house fly diverged. The diet, ecology, reproductive strategies, and mouth parts of modern mosquitoes and house flies are radically different. I’ve done work on mosquitoes and their evolution is (unfortunately for half the world’s population) very interesting. They are arguably the worst spreaders of disease, being vectors of malaria, dengue fever, yellow fever, chikungunya, West Nile, several different encephalitis-causing viruses, and heartworm. Insecticide resistance is exploding and speciations are being observed in disease vector mosquitoes. Climate change is permitting formerly tropical mosquitoes to move into new territories and new speciation events are inevitable. Sure someone could protest that they’re still bugs with six legs, but then humans and turtles are still just tetrapods and those have been around for almost as long as insects.

Murphy's Law, that brash proletarian restatement of Godel's Theorem. -- Thomas Pynchon, "Gravity's Rainbow"