Welina!

My name is Sergey V. Zubkov, and it is my web page that you’re now viewing.

I’ve been a writer, a teacher, a chemist (that’s what my degree is in), a biochemist, and a software engineer. I live in the USA and I love the Internet and the endless possibilities of communication that it offers. I’ve been online since 1995 and never regretted the hours spent on the IRC or other communication systems.

The role of this website is dual: it is my new blog (accessible via categories above) and it is contains the bulk of my little philosophical web page Cardinal Knowledge (accessible via pages on the left).

Saturday, January 24th, 2009 at 21:25

Things I won’t work with, either

I was randomly linked to an awesome blog of an organic chemist who wrote, among other things, several posts titled “Things I won’t work with”. Here: http://pipeline.corante.com/archives/things_i_wont_work_with/

Even if you’re a non-chemist, you will appreciate the compounds that can force evacuation of a village when their scent wafts over from an open flask in a nearby college, compounds that set concrete, sand, bricks, water, and people on fire as they happily burn through them, or compounds that just blow up while standing undisturbed in the dark at cryogenic temperatures.

Fun stuff.. And no, I didn’t work with any of the title compounds either :)

Crossposted from Livejournal

Friday, March 5th, 2010 at 19:01

february 2010 in science

So, this is what february 2010 added to the collective knowledge of humankind:

Chemistry
A 1 GHz NMR spectrometer (that’s 23.5 Tesla) was brought online in Lyon, the new long-awaited record after Bruker 950 MHz spectrometers appeared in 2006. It costed over 11 million euros, so don’t expect your college getting one soon. Speaking of NMR, the largest ever distance between two nuclei, 14.4 A, was measured with tritium-labeled MAS NMR (normally, your regular biochemical 1H liquid state NOE NMR measures only up to 6 A).

Also in chemistry, where dozens of new reactions are developed every month, two remarkably simple ones were made in February: a zinc-catalized reduction of amides to amines which tolerates alkyl, aryl, heterocyclic, esters, ethers, nitro, cyano, azo, and keto substituents, touching nothing but amides. The other one is a one-pot synthesis of 1,3-disubstituted allenes from a 1-alkyne and an aldehyde.

By the way, someone finally made a fullerenium salt, C60(AsF6)2, and it turned out to be a regular semiconductor instead of the speculated high-temperature superconductor.

Also someone ambitiously claims to redefine the textbook definition of H3O+ in water, based on IR, but I don’t see how this agrees with the 2005 fast scale study and a host of others.

A superheavy isotope of carbon, carbon-22, was found to be more stable than expected, and very hard to analyze with current theory. And finally, the element 112, produced back in 1996, was finally given the official name Copernicium, and chemical symbol Cn by IUPAC. Update your periodic tables!

Physics
While LHC’s full run is getting delayed until 2013, RHIC (our own, Long Island based black hole generating doomsday device) is proving it can still do cool stuff — analysis of 200 GeV quark-gluon plasma gave new hypotheses for barionic asymmetry and the large magnetic fields of the galaxies.

Also in the world of physics, a saser (a laser analog emitting sound waves) was finally made, in two different ways, by two groups simultaneously: in California and UK. Very cool things, hopefuly they’ll find use for them.

Another hardcore physics study, the crossover from BCS superfluid (weakly interacting pairs of fermions) to BEC supefluid (tightly bound bosonic molecules made of fermions) was studied with anticipation of something new and cool but was found to be boring fermi fluid.

And more physics: the 100 year old Abraham-Minkowski dilemma about the momentum of light was finally solved: both are correct.

Biology
A new oldest life form on Earth was found and dated to 3.2 billion years ago.

Yet another psychology research in the origin of religion shows that moral judgments are not related to religious background. At the same time, neuroscientists noticed that when they remove a chunk of rt. inf. parietal cortex (normally providing spatial awareness), patients gain self-transcendence.

Speaking of neurophysiology, although the “facilitated communication” for that belgian in persistent vegetative state turned out to be a hoax (as anyone familiar with the idea should have known), a group of researchers who used fMRI in 2006 to get answers from a vegetative patient scanned 53 more and found that four of them also have distinct brain activity patterns in response to questions.

And, for something weird, bees can recognize human faces.

Crossposted from Livejournal

Monday, March 1st, 2010 at 13:08

DSM-V

Oh, hey, temper tantrums, Restless Leg, binge eating, and cybersex addiction and other excessive sexual activity, are gonna be mental disorder in the USA now. Good thing Internet addiction didn’t make the cut due to insufficient evidence :)

Crossposted from LiveJournal

Thursday, February 18th, 2010 at 07:43

science review for january 2010

Running a little late here because I spent this week in the humid warmth of McAllen, TX, and I probably miss a few cool things.. but anyway:

in chemistry news, An isomer of href="http://www.sciencemag.org/cgi/content/abstract/327/5965/564">hexasilabenze was created, Si6R6, which turned out to be tricyclic (and bright green). It apparently is aromatic in some loose sense, and the authors want to call this ‘dismutational aromaticity’. Before this, only hexasilaprismane has been made, of all the Si6R6 isomers, and it was definitely not aromatic. Also, a quantum computing team calculated energy levels of hydrogen molecule to 20 bit precision using photonic quantum computer. Would be nice to be able to do quantum chemisty calculations on large molecules one day.

in physics, the 80-year old bizarre prediction of Dirac’s relativistic QM theory called “Zitterbewegung” was tentatively confirmed by a no less bizarre technique called ‘quantum simulation’, where hitting trapped ions with fine-tuned lasers makes them behave as free particles moving at fast speeds or as other types of quantum systems that are being simulated.

Speaking of the bizarre, biology was rich in that last month (when isn’t it?). Researchers attempted to tag some tree frogs with radio transmitters and learned something really weird: Tree frogs are apparently able to move into the bladder and urinate anything that was lodged in their body cavities: thorns, insects, radio transmitters. Also, a parasite was found, appropriately named Endaphis fugitiva, which jumps out of the banana aphid in which it lives when it realizes the aphid is in the jaws of a predator.

In promiscuous (but not in monogamous) mouse species, sperm cells can recognize and team up with sperm cells of the same male or, in a lesser extent, sperm of a brother. They form packs that swim faster than a single sperm cell. Also a couple researchers from Cincinnati decided to circumsize fruit fly males with lasers to see if their penis ornaments help them in mating.. Obviously, they do.

Speaking of sex, early last month a group from London made CNN news when they claimed that there is no G-spot in human females, simply by asking a whole lot of twins if they think they have any, arguing against an earlier italian study where G-spot was actually located with ultrasound.

And of course as everyone knows, paleontology had two major discoveries to hit the news: A polish group found well tetrapod tracks in Middle Devonian, showing that tetrapods coexisted with elpistostegids (such as Tiktaalik) for over 10 million years in different niches. Some chinese paleontologists found melanosomes in fossil dinosaur feathers, suggesting that dino’s plumage was striped russet-orange and white, overturning the idea that the color of prehistoric animals would never be known. How if they could find fossilized voice…

Something cool about humans: Ever seen movies where cowboys duel, the bad guy draws and the good guy reacts and draws faster? There’s truth to that: human brain reacts faster than acts (by a small margin, and with more mistakes, but faster). Another curous find about us: barefoot running subjects humans to four times less stress than shod running. Shoes make it easy to pick up the bad habit of landing on the heel.

And finally the poor little Mars explorer Spirit, stuck in a sand pit with two broken wheels since November, was finally declared a “stationary research station” (also covered by xkcd).

Crossposted from Livejournal

science review for december 2009

Now that I’ve sufficiently recovered from the New Year celebrations, let’s see what did the humanity learn in the past month.

In chemistry, carbonic acid, H2CO3, was finally observed experimentally in solution. Speaking of simple targets, a teraherz study of water showed that dissolved ions neither weaken nor strengthen water’s structure, and yet another study of caged water clusters showed how some can dry up and get rehydrated back. Another entertaining non-nano chemistry work, cyclooctatetraene was forcibly planarized and the resulting antiaromatic molecule studied experimentally. Closer to my interests, solid-state NMR can now be used to determine structures of nontrivial proteins and a new solution NMR sequence, HN(COCA)HAHB, was developed to study unfolded proteins. Finally someone seriously cares about coupling constants in protein structure analysis.

In non-nano physics, mass of top quark has been ascertained to about 1% error. And in a rather groundbreaking quantum physics news, the 40 year old hypothesis of the universality of Efimov trimers has been experimentally shown to be true last month by the Hulet atom cooling lab in Rice U (cute picture of a high-five from Efimov to Hulet there). The first Efimov trimer itself was only observed in 2006, but this group confirmed the universality property and even observed Efimov tetramers.

In biology, airflow inside dog’s nose was studied: we now know that they smell with each nostril separately (like we hear sounds with each ear separately), and that they do not exhale scent when exhaling air. Microbiologists now know of a new giant virus from amoebae, although it doesn’t surpass Mimivirus. Another group, while studying rock-breathing bacteria, figured out how they create biological “wires” that pass through the cell wall and conduct electricity between the cell and the rock.

Psychology had a couple if interesting findings: a group of Swedish psychologists noticed that the time it takes for a newborn mammal to walk can be exactly calculated based on adult brain mass and gestation time, and that humans are not at all exceptional in their motor development. In more practical news, NYU psychologists demonstrated on human subjects that it’s possible to completely erase fear attached to a memory if it is modified at reconsolidation time, as was known to be possible in rats (if you didn’t know, after we recall any memory, there’s a moment a few minutes later when it is being reassembled to be put back in permanent storage, and it can be forever modified or even erased at that point). Speaking of memory, someone at Case Western studying short-term memory managed to store information in vitro, in pieces of mammalian brain tissue.

Astronomers finally found an unambiguous example of a pair-instability supernova, in another galaxy, naturally. In less distant news, Cassini was able to get a good look at the humongous planet-wide hexagonal cloud on Saturn, first spotted back in the 1980s by Voyager.

And finally, in geology, the old and somewhat disputed deep mantle plume hypothesis gained solid experimental support with a new study of Hawaiian hot spot.

Also, in case you feel guilty about drinking champagne at New Year’s eve, it is just as good at preventing cardiovascular disease as red wine :)

Almost forgot, last month’s animal behavior brought us the tool-using octopus and the explosive duck erections!

Crossposted from LiveJournal

Wednesday, January 6th, 2010 at 12:02

Global warming denialism.

We’ve had a surge of anthropogenically forced climate change denialism lately, the stolen email incident even made it to Daily Show (the only news program I watch). In case anyone’s doubted, they have exactly as much scientific credibility as AIDS denialists or the “vaccination causes autism” movement.

Of course, quite a few politically-motivated environmentalists made stuff up where science was too boring, but even Al Gore’s infamous “Inconvenient Truth” has ten times less factual errors than one global warming chapter of Lomborg’s “Skeptical Environmentalist”. Personally, I think pressuring people into feeling environmental anxiety and guilt is just as amoral as slandering climatologists (actually, I think a rational person should never experience guilt at all), but whether people deny or stretch the observed facts doesn’t change the facts in the least.

And since I’ve been running into internet discussions about this issue here and there, here are a collection of rebuttals by topic, partly for my own reference.
Responses to common contrarian arguments at RealClimate, the most in-depth blog on this topic, since it is ran by actual climatologists: Gavin Schmidt, Michael Mann, and others.
How to talk to a GW skeptic at IllConsidered, blog by Coby Beck, an AI software engineer.
Skeptic Arguments by taxonomy at SkepticalScience, blog by John Cook, a solar physicist.
Climate Chainge: A guide for the perplexed by New Scientist magazine, bad as it became.

Crossposted from LiveJournal

Tuesday, December 22nd, 2009 at 13:17

science review for november 2009

It’s been four years since my last scientific publication, and while C++ is all good and profitable, I feel like I’m missing the fun stuff. So I randomly decided to check the news to keep myself informed.. Let’s see what we’ve learned in November 2009, other than that the Moon is slightly damp and that LHC finally works.

In chemistry, everyone who was crazy about fullerenes and nanotubes is now crazy about graphene (monolayer of graphite, first literally peeled off a chunk of graphite with Scotch tape by some russians in 2004). In just last month people kept coming up with new ways to create it, new ways to modify it (and some more), new ways to calculate it, and new physical properties to measure. That whole nanoscience thing is a good source of funding!

Adult neurogenesis (did you even know new brain cells are constantly born in adult brains?) is still a hot topic in neuroscience: these japanese guys say the new brain cells not only form new memories (as a bunch of 2008 works has shown) but also clear out memories from hippocampus after they’ve been permanently stored in neocortex. Speaking of memory, this girl just showed that motor skills are stored by permanent rewiring of neurons, which is a neat explanation for why once you know how to ride a bicycle, you’ll never forget. Also, speaking of brains, there was this cool review by the leading bee brain specialist (who once was a postdoc in Stony Brook, like me) saying that brain size does not change cognitive capacity.

Continuing the search of minimal set of molecules required for life, a crowd of biochemists from all over europe finally published their detailed analysis of one of the smallest bacteria, Mycoplasma pneumoniae, in three articles in Science: 1, 2, 3. They found it “more subtle and intricate than was previously considered possible”. Well duh, it’s a pathogen, it has to be able to change quickly, and under evolutionary pressure to be small it just had to reuse the same molecules in multiple ways. One thing evolution is good at is reuse. It’s a good reminder of how dismally far is biochemistry from understanding the function of nearly all proteins. Decent advance, nevertheless.

What else.. Astronomers, besides everybody’s favorite slightly damp Moon bombing, found out that heliosphere is not smooth but has a weird ribbon going around it: Science 326:959 and four more papers in the same issue (how do they get so much space there with nothing but guesses??).

Anthropologists, who had a bit of a debate about the 3′6″ tall hobbit named Flo (Homo floresiensis, fossil human-like specimen found in 2003) have a new article, from Stony Brook of all places, again saying it’s a real specimen and not a sick H.erectus.

Botanists discovered some altriustic plants (they change their morphology to cooperate with relatives and to compete with strangers growing nearby), and some plants that use camouflage to hide from herbivore animals. Who knew botany can be interesting?

In kick-ass geological news, African continent is being torn asunder, with the gigantic Ethiopian Rift which suddenly appeared in 2005 in the middle of a desert, becoming 35 miles long and 20 feet wide in just a few days. It is now believed that it is no joke, this crack will one day become the middle of a new ocean.

And just for fun, someone bothered to find out why a dash of flour tossed on the surface of water scatters out so very fast (hey, it’s nanoscience!), and these girls say they got a good idea how to make the infertility pill for men.

Crossposted from Livejournal

Tuesday, December 1st, 2009 at 21:20

Fruit bats and their tongues

Fruit bat fellatio

Tan M, et al. (2009) Fellatio by Fruit Bats Prolongs Copulation Time. PLoS ONE 4(10): e7595


I know it’s two weeks old, but it’s still amusing. To quote the article, “Our observations are the first to show regular fellatio in adult animals other than humans.”

What I find really funny though is how unrealistically precise they were with their timing. Duration of copulation measured to one hundredth of a second? Really? With precision of give or take half a minute?

“The average duration of penis licking was 19.14±3.45 s, representing about 8.7% of the average duration of copulation (220.29±26.19 s (N = 14)). [...] The pairs spent more time copulating if the female licked her mate’s penis [...] than on occasions when females did not show licking behavior (121.83±20.56 s, N = 6)”

Well, I guess that’s PLoS ONE for you.
Crossposted from LiveJournal

Sunday, November 8th, 2009 at 20:08

Li Wei

On the Earth surface, Li Wei, 2009

"On the Earth surface", Li Wei, 2009


I totally forgot on whose lj (if it was lj) I saw a link to Li Wei’s photography, these days I’m so busy at work I cannot remember what I had for breakfast. But hey, he’s pretty crazy with his imagination and the ability to take a picture like that with no photoshopping. Even though he has a bizarre habit of falling into things head first – he makes one lousy superhero.
Crossposted from LiveJournal

Friday, September 4th, 2009 at 14:07

Microscopes show C-H bonds now O.o

Pentacene image from IBM press release
Pentacene image from Science 325, 1110 (2009)><br />
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As <a href=BBC reports on this article in Science published by a bunch of crazy IBM researchers from Zurich, atomic force microscopes can be tuned so insanely well now that even C-H bonds become (kinda) visible! (the molecule on the picture is pentacene)
Crossposted from LiveJournal

Monday, August 31st, 2009 at 17:25