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Nervous in San Diego writes:
Dear Professors of TWiM,
I was recently introduced to TWiM by a neighbor. For the last few weeks I have been listening to the backlog of TWiM podcasts, mainly while walking our dog. Regrettably, our dog is a lousy conversationalist. Listening to TWiM while walking is therefore a major improvement. As we walk, the dog investigates things I can not see, while I listen to you talk about them.
Because I have no background in microbiology I must deduce the meaning of the five, six and seven syllable words that you use so effortlessly from the clues provided by the occasional simpler words that surround them. I think it is fair to say that microbiology is the study of what can not be seen using words that can not be pronounced.
The other day our dog and I were listening to a TWiM podcast. (In truth, I was listening and she was otherwise occupied.) You were describing how some parasites modify the behavior of their hosts to the advantage of the parasites. Because I was nearing the end of our walk — and the podcast was not yet complete — I decided to take another lap around the block.
It suddenly occurred to me that TWiM was modifying my behavior. My decision to extend my walk seemed substantively the same as the behavior of a grasshopper afflicted with Summit Disease. As I continued thinking about this phenomenon, I surreptitiously checked my mouth for evidence of frothing, while resisting the urge to climb a telephone pole.
Fearing the worst, my first thought was to rip off my earphones to rid myself of the TWiM infection. But, before taking such a drastic step I decided to solicit your expert advice.
Questions: If listening to TWiM is capable of causing me to walk further, is it possible that you are also inducing behavior changes that I have not yet recognized? Will I soon start craving pickles or become addicted to reality TV? Would it be safer for me to restrict my future podcast listening to Car Talk? I await your response with some trepidation.
Nervous in San Diego
P.S. The weather here seldom changes, but I’ll leave it to my neighbor Elio to provide the details.
Hello, This Week in Microbiology,
First of all, your podcast is amazing, it made my microbiology preparation much easier in university and got me curious about many things.
Now, I've listened to the battle for iron podcast and one thing that I couldn't find on Google got me interested. What is the exact etymology of 'ocelloid'. It was mentioned the word has something with "eye" inside of it and I had to look it up but nothing really came up. Do you by any chance have any idea where it might have come up from?
Thank you in advance,
keep being awesome!
Best wishes from Bulgaria.
In response to the letter from Mark:
Besides West Nile and other mosquito-borne illnesses, fungal diseases leap to mind. Dry soil becomes dust that can be inhaled. Coccidioidomycosis (aka Valley Fever) is probably most relevant to California. There is an open access systematic review available from Plos Currents that may be of interest.
Alice I. Sato, MD PhD
Pediatric Infectious Disease
Albany Medical Center
PLoS Curr. 2013 Jun 5;5. pii: ecurrents.dis.7a2cee9e980f91ad7697b570bcc4b004. doi: 10.1371/currents.dis.7a2cee9e980f91ad7697b570bcc4b004.
[Mark had asked: How do drought conditions change public health risks? CA is now experiencing higher incidence of West Nile virus infections (TWiV listeners will recall Prof Despommier has explained mechanisms coupled to drought and mosquito habitats several times). Should other risks be expected? Or shifting between risks?]
For your interest in listening to physics, there is a podcast called The Titanium Physicists Podcast. They use a conversational format similar to what you use. They have a panel of experts and a guest who is not a physicist but who is accomplished in some other area. BTW I recommended the twix group to him when he was looking for a biology podcasts.
Love the 4 podcasts you people do.
Hello TWIM overlords,
I have been listening to this podcast since it first came out in 2011. Now I am an incoming senior at UC Berkeley majoring in Microbial Biology. It was your podcast that helped me decide what to study. I would also like to say hi to the graduate student that captured fruit flies with wine; perhaps we have already met.
It's summer for me, and I have been re-listening the podcast. Everything is glorious, but what caught my attention is TWiM #48: It's all about direction with Jo Handelsman. This was released in 2013 and it talked about the deficiency in science educated workers in the bachelors level. I was hoping in working in a startup or in industry for a year or two before I went to grad school for a phD, but should I bother at all? I don't plan on going to academia, and I don't know what to do about further education. My grades are not the best but I'm a student researcher in a lab up in the hill and I enjoy research. I have a lot of autonomy in what I can do and I'm afraid I'll never regain that sense of freedom without a phD -- at the same time, I don't want to get lost in constant paperwork. Berkeley has a lot of academics so I don't know what it's like in industry. I do enjoy it when you guys bring it up in the podcast.
This podcast was the fodder to keep me going through bad semesters. At first, they all seemed fascinating and quite confusing. Now I understand more, but more importantly, I'm questioning the paper and thinking about what the data means. I still have a long way to go, and in a way, I feel like I have learned nothing because there is always so much. I would like to thank all the hosts of TWiM for being part of my high school and college experience. I still have a year left in college but I should have thanked you three years ago when I first got accepted.
Kathy Spindler writes:
In the late 1970s, when there were a couple of years of droughts in California, the complete saying was, "If it's yellow, let it mellow. If it's brown, flush it down." And a very memorable billboard I saw in the Central Valley showed someone in the shower with the caption, "Sing shorter songs."
I enjoyed crossing over to TWiM 104 to hear the measles story covered!
Hi Vincent et al,
I was just listening to your TWiM 41 interview with the HealthMap man, and called it up, to have a look. There were a couple of red dots, not far from me--one a mystery illness making an EasyJet plane turn back home--and the other, this shocking news about the, endangered, Saiga, antelope. It does not seem that long since I was watching wildlife programmes that featured migrations of, seemingly, limitless numbers of these animals: now we hear that they are being wiped out with extraordinary speed, by what is thought to be a bacterial infection.
It seems to be happening almost impossibly fast. Perhaps the team would like to look into it for your podcast.
All the best,
Weather still rather grey and windy (But I don't get out, as I'm housebound with ME, and can only stay upright for a few minutes at a time.).
[also see Zimmer article: http://www.nytimes.com/2015/06/02/science/saiga-antelope-mystery-disease-die-off.html?_r=0]
Loved your SNP. In addition to washing produce, only reverse your stomach's HCl when necessary. (Also, the STEC dose is lower than Salmonella.)
Wink Weinberg (Atlanta)
Greetings from sunny Seattle! Where its 21 degrees C with clear skies.
Because you asked...Here are my 2 cents on the whole handwashing situation that has been discussed over the past few episodes.
My solution would be to change building codes to require shared sinks for men/women that are located outside the actual bathroom.
This would ensure compliance because it would allow for policing without violating any privacy issues. It could be especially effective in a restaurant setting where a manager could simply discipline employees they watch leave the restroom without making the required stop at the handwashing station located outside.
Additionally, some peer pressure and social stigma would be enough to guilt people into not skipping the handwashing station. Behavior might change if poor hygiene is on display for everyone to see.
Thanks for the great podcasts! I am a fanatic Twiv/Twim fan and listen to the podcast on my 1 hour commute to my job in a manufacturing lab @ a biotech company.
Long time listener, first time email-er.
Greetings podcast team,
I'm a long-time listener to TWIM and TWIV and if I had a longer commute I would get TWIP in the mix too. Only so many hours in the week!
I am a research tech in Portland Oregon, where our dry mild winter has given way to a gorgeous dry mild spring. Currently 57F and sunny. 2015 to date has been bad for farmers (and skiers) but pleasant otherwise.
I wanted to commend you all for taking on papers and questions outside of your specific areas of expertise, because the conversation that ensues lets us listen in on how you think about science questions.
If you had all the answers at your fingertips it would be highly accurate but of less interest and utility for me at least.
I wanted to weigh in on the mandatory handwashing sign question because I think it is a Trojan horse. Libertarian politicians and letter writers claim they want to see freedom of choice for consumers so free markets can make everyone's lives better but the handwashing argument is a pretty clear tell regarding their true intentions.
Since handwashing is the slightest of inconveniences to the restaurant worker and has no downside for the consumer, it's hard to believe that they are truly driven by their desire to be able to buy a meal at a restaurant where the employees have not washed their hands.
I am convinced until I see some persuasive arguments to the contrary that each time you hear about this free market handwashing topic the real motivation of the person putting this idea out in the culture is to normalize the idea that government in general and regulation in particular is bad, and they really care about their favorite business interest believed to be oppressed by Washington, not oppressed cooks who'd rather have dirty hands.
What I'm really curious is how the independent certification would work. Why are third party monitors watching us wash up better than a government mandated sign? If the government was keeping an eye on us in the bathroom they'd be marching in the streets!
Hello again - I just listened to the Red Queens discussion about iron battles on TWIM 103. Regarding your interest in other occurrences of this phenomenon there is a paper by Roy Jensen et al at http://www.ncbi.nlm.nih.gov/pubmed/?term=24616884 where he discusses in detail the battle for tryptophan between Chlamydia and their mammalian hosts.
Its warm and sunny Spring weather here in California’s Bay Area. The fourth year
of Drought is upon us - please send water.
Speaking of water, below is a humorous incident that could be used to draw
attention to MRSA or proper hand hygiene. These are probably better suited to
informal settings like the bar instead of the classroom, but here goes ...
A town in Texas televised their 4/28 city council meeting. The mayor recognizes
the mayor pro tem who starts to talk about raising MRSA awareness in their
community, sharing personal experiences with MRSA victims.
The mayor leaves, and the mayor pro tem continues to talk. Male urination sounds
can be heard and snickering starts. A loud flush is heard and the mayor pro tem
erupts in laughter, which continues as the mayor returns to the council room. He
obviously didn’t wash his hands.
Within days a video clip “went viral”. My friend sent me the link 5 days later.
When I saw it on YouTube it had 1.3M views. The Houston TV news picked it up -
watch it here: http://cbsloc.al/1JLDdAk
This real life event quoted from the venerable, sophomoric movie “The Naked Gun.”
Detective Frank Drebin (bio: http://bit.ly/1R6Tpyc ) had a similar, highly
fictionalized urinary mishap with an open mic:
Fortunately TWiX shows are produced with tethered microphones.
Speaking of drought: in California 80% of the water supply is used by
agriculture. Our now, maladapted water policies reward growing high water
consuming crops, like almonds or rice, for export . CA Governor Jerry Brown has
declared a water emergency and is seeking to have households reduce usage in the
range of 25-33% compared to 2014.
People who support conservation efforts have a handy phrase “if its not brown
don’t flush it down.” People critical of the governor have morphed this into
“it its Brown then vote it down”.
Let me end with a serious question:
How do drought conditions change public
health risks? CA is now experiencing higher incidence of West Nile virus
infections (TWiV listeners will recall Prof Despommier has explained mechanisms
coupled to drought and mosquito habitats several times). Should other risks be
expected? Or shifting between risks?
All the best.
For anyone interested in trapping fruit flies without drowning them, you can put a little wine (or I use a piece of overripe banana) in a container with a small hole in it. The flies get in but can't usually find their way back out. You can then take them outside and release them. Every now and then when the contents are particularly alcoholic smelling, it seems to me like the fruit flies are slower to fly away... as if they were drunk!
I was glad to hear someone write in in favor of your using the word Talmudic for your questions. It's really the perfect word for unanswerable questions that are worth asking just for the thinking. This atheist also approves. Talmudic questions and midrash are traditions more people should know about just because having a questioning culture is an important and useful thing, I think.
Thanks for all you all do.
I have a few observations and comments about the TWiM 101 and 102
letters about hand washing rules.
1. In his book _Fast Food Nation_ Eric Schlosser discusses the
relative abilities of regulators and consumers to change food safety
practices. Consumers were a powerful force cleaning up
slaughterhouses because there was a media frenzy after the Jack in the
2. The bathroom sinks where I work dispense a trickle of cold water.
If you let them run for 5 minutes you get a trickle of warm water.
Pathogenic bacteria are laughing all the way to the kitchen. "Green"
building rules may make the hand-washing debate irrelevant.
3. In my experience doctors and dentists wear gloves but do not wash
their hands in my presence. Freakonomics covered the difficulty of
getting doctors to wash their hands:
4. The traffic law analogy on TWiM 101 leads to the opposite
conclusion than the one proposed.
You can build a road network without signs and signals. In Europe the
term "naked streets" is used for unregulated urban areas. They work
as well as hyper-regulated American streets.
We keep forests of signs around for comfort, because people
erroneously think "it can't hurt." It can hurt. There are books of
guidelines for predicting whether road signs help or hurt. Traffic
engineers don't follow the books because the boss already "knows" more
regulation is better. When you start "this week in transportation
policy" I'll write a few thousand more words for you.
Lawyers use terms like "penumbral crime" and "aspirational law."
These are laws that aren't expected to be obeyed, aren't taken
seriously, and teach us that we have to decide for ourselves which
laws to obey. Everybody who drives breaks the law, and I include
those who say and even believe they don't.
Inspectors can enforce laws requiring signs saying "hands must be
washed." They can not enforce laws saying hands must be washed.
Given that we have a finite number of inspectors, what do you want
them spending their time doing?
Hey Vincent, Elio, Michele and Michael!
I'm a first year microbiology graduate student at UC Berkeley and an avid listener of twim. Elio's snippet from the most recent podcast reminded me of a personal anecdote that might be useful to share with listeners. The snippet was about the volatile compounds produced by yeast that attract fruit flies and cause dispersal of the yeast. A couple months back I had a small problem with fruit flies in my apartment and decided to try the home remedy of apple cider vinegar and soap to get rid of the flies. The apple cider vinegar is supposed to attract the flies while the soap breaks the surface tension causing the flies to become stuck and eventually drown. This concoction helped get rid of some of the fruit flies, but there were still a few buzzing around after a couple days. That weekend my roommates and I drank a bottle of wine to help de-stress from the hardships of graduate school. We left the bottle out on the counter with only a couple centimeters of wine left in the bottom and the next morning it was filled with fruit files! It seemed that the volatile compounds in the wine were much better at attracting fruit flies than the compounds in the apple cider vinegar.
It was very interesting to hear about the molecular basis for this aroma-based communication between yeast and fruit flies. For any listeners who have come back from spring break or a weekend away and now have to deal with fruit flies I would recommend using this wine trap! It seems a little bit evil to be luring fruit flies to their death with the scent of a presumed feast, but it works beautifully!
Anyways, keep up the good work guys! :)
I can't believe I'm writing in about this, but I have to say that I was rather deeply offended at listener Dave's insistence on policing your use of the word "Talmudic" on TWiM.
I am a religious Jewish scientist. Part of my experience is the understanding that my colleagues, who often discuss their Christianity, Atheism, Buddhism, Islam, Sikhism, Taoism, Shintoism, and other religious -isms, are as tolerant and respectful of my Judaism as I am of their beliefs.
Science is a human endeavor, and scientists have beliefs and cultures. These do not affect the judgment of a professional scientist, but having diverse cultural perspectives and an uncensored environment is an asset to scientific pursuits.
Silencing religious, or even formerly religious, scientists stifles the pursuit of science. Science should take all comers provided they pursue unbiased interpretation of data. There is nothing about the word "Talmudic" which implies you'd pursue anything else.
The Talmud is an ancient Jewish cultural artifact. It preserved many of the basic logical techniques of the Hellenistic world, and was a building block of the intellectual tradition that gave birth to modern science. My own studies of the Talmud taught me to value the importance of free inquiry and discussion that relies on evidence and logic.
There are enough places where Jews face harsh consequences for speaking the words of our culture or sharing our intellectual traditions. I have gravitated to science in part because I feel safe among intellectuals who respect the value of my ancient culture.
I enjoy TWiM partly for its "Talmudic" questions, which remind me of the long, unresolvable arguments that I learned as a child. It's a quintessential rehearsal of science: the exploration of questions that we know we will never answer to our satisfaction, but that are explored because of the invaluable lessons that will be revealed for the asking.
It makes me smile and feel welcomed every time I hear Dr. Schaechter say "Talmudic Question." I would hate to see a fun and enjoyable exercise be marred by the views of a listener who cannot tolerate a single word from a culture that differs from his own. I would never have complained about an "Atheist Question" or a "Madrassa Question." I am appalled that Dave would think it appropriate to scold you and attempt to police speaking in a way that is informed by your participants' culture.
Thanks for all the work you do, and I am sorry if anything I've said is impertinent. I just couldn't believe what I was hearing when you read Dave's letter.
Dr. Vincent and the Twixers,
At some point this sudden wave of deaths in a small southeastern Nigerian town might become a potential twix topic (see link below) unless it turns out to be poisoned food or water. Separately but instigated by this, a thought-question occurred: as unlikely as it may sound, are there other vectors besides viruses, microbes, parasites and poisons from known toxins that could be "contagious" and which could kill quickly? For example could somebody use CRISPR-CAS9 to modify a common benign bacterium to deliver a toxin? Ugh.
Fanboy of TWIX,
Contagion MAP -- A brief history of malaria, leprosy, and smallpox.
I don't know if this is accurate or if it's been featured already, but
perhaps it might be of some interest for TWIM.
And this is a few years old and again I don't know if it's already been covered.
ENDEMIC LEPROSY IN NEW YORK CITY
I first want to compliment you on one of my most listened to podcasts, and one that I actually know what is being presented most of the time.
Now about the term Talmudic.
Do we need a name that is a legal commentary on the Torah, explaining how its commandments are to be carried out., all 613 of them, on a science podcast?
Religion is so prevalent in everything in society, from media, politics, holidays, and visual statements that are overwhelming.
The liberal view of the "belief in the belief in religion" is not questioned (as Dennett has explored).
But please, don't let it creep into the sanctuary of sanity and reason that is TWIM.
In my experience working in food service, you're all right. There's no good way to mandate and police handwashing. But that's not really the way it works, anyway. The education is mandated and best practice rules are set and when the regulatory agencies check up on you, they take points off for each thing that doesn't measure up. And it's true that the rules aren't followed perfectly, but if you aren't doing well enough you get corrected or closed down before your customers even notice most of the time. Without the rules, believe me, a lot of people would go with the "well I don't do this at home and it's never hurt me" philosophy and things would be even dirtier than they are. It's true that when enough people got sick you'd lose customers. It's true that in the end the free market would probably take care of each individual case. But the free market is a lot slower than regulation and tends to require more hurt and death to create change. It's also true that without regulation private groups often jump in to fill the void. But we often have less influence when we try to make change with money rather than votes and due diligence is often difficult at the individual level. Everything requires more participation than US citizens are interested in these days to keep things running smoothly and well. It's just as easy to relinquish your personal responsibility to the "free hand of the market" as to the idea of government as something there to take care of you instead of something we all are supposed to be a part of.
P.S. The health departments that are in charge of enforcing the code are not staffed by the restaurant industry. Other enforcement agencies don't need to be staffed by members of industry, either. Scientists and people from a more academic side of the fields would know just as much as business owners and employees. It's just been policy for a while now to allow the revolving door between industry and government jobs.
I am a retired computer programmer and also a free market libertarian. I listened to a recent podcast where the subject of mandatory hand washing by food workers was tossed around. I would like to present a few more of the free market arguments on this subject.
1. With a government mandate to wash hands, what makes you so certain that this mandate will in actuality have the effect that food workers a) obey this rule (especially if there’s nobody watching them in the rest room) and b) that they will do so effectively. I’ve heard that within some short time (minutes say) after a wash, bacteria quickly repopulate the hands say when the water is turned off by touching the faucet, or a paper towel dispenser with a slider is used to dispense towels. And since there’s no requirement for customers to wash, what happens when they touch the doorknob and a worker touches it after washing.
2. If there were no government requirements for washing or inspections, don’t you think there’d be a niche for some certification agency (like a consumers guide) to take up the job of inspecting facilities. We all use many electrical devices and these come with ratings from a non-government agency; we’ve all seen UL approved appliances. Rather than a sign stating we don’t wash hands, how about one that says UL certified or some such. If such a sign were displayed fraudulently, then even in a free market culture this would be a criminal action. Free markets still have rules against force and fraud known as the non-aggression axiom.
3. When the government regulates an industry, this tends to make people complacent and to not do due diligence. We see this quite evident in the financial markets. In addition, the industries being regulated tend to get regulations that keep out competition more than anything else. And where do you think the regulators come from if not the industry itself? There’s much incentive for fraud here.
4. If you and your friends keep getting sick after eating at a particular restaurant, don’t you think the word will spread and thus weed out the bad establishments?
5. Surely, doctors and hospital workers must be quite aware of the issue of cleanliness, yet in my own personal experience, I almost never see a doctor wash his hands before or after an examination. What is so special about food services? Why is there no sign at the doctor’s office requiring washing of hands?
There are many more points I could make, and these have been made by more articulate writers than myself in the libertarian community. One of the best writers is the late Murray Rothbard. I would suggest some of his works, but in truth, rather few people seem to be interested in the subject. But nearly anyone would be better than some lying politicians, but then I repeat myself.
I find it almost universal that anyone in the fields of research tend to assume that there is simply no alternative to the government when it comes to funding. I’m sure you all have numerous cases of waste that arises from this form of funding. In a free market, universities would self fund their research, and then perhaps create documentaries to pay for the research. I’m sure you all have seen how political favoritism influences who gets the grants under the government system. The reason I’m still not convinced by the climate change arguments is that I challenge you to find some climate change skeptic being funded by government.
I see no reason to believe that food workers are being regulated any better than any other line of work.
However, I still love the podcast, although my favorite is TWIP; I especially like the new format with case studies. Keep up the great service.
I wonder if your team has anything to say about the prevalence of salmonella in seed foods.
For some years, I have been getting regular notifications from the English Food Standards Agency, when seeds and seed products have been withdrawn due to the presence of salmonella.
What made it all the more puzzling was that, despite the huge furore there had been over salmonella in eggs, the UK media, seemed not the slightest bit interested that so many other foods were still being regularly withdrawn due to salmonella contamination. I did ask the FSA to explain this attitude, some time ago, but it really didn't seem to bother them.
Today it was melon seeds that were withdrawn. When it was the more usual sesame, I could imagine that there might have been bird droppings on the plants, but I can't see them getting inside a melon seed!
Perhaps your team might enlighten us as to how salmonella gets into seeds, and why nobody seems to get poisoned by it when it does!
All the best,
Incidentally, my Blackberry can't move the captcha image about. :(
Varun CN writes:
First, congratulations on reaching the TWiM 100 Landmark and wish the crew the same success that TWiV currently enjoys. I also want to vote up for Elio's latest idea of bringing in "Talmudic questions" as a part of TWiM discussion. I want to punch in a couple of opinions.
Microbiome, a product of big data science has been a topic of great discussion. Recently Eric Lander visited us and during the interaction had brought up this topic. Microbiome is a dynamic phenomenon and variation between individuals is far more than what actually was predicted earlier. The understanding is that Microbiome can change in the same individual depending on environmental factors.
This discussion brought in 2 questions
1. Do we know enough about the direction of cause and effect in microbiome context
2. How to account for the variance in microbiome and its effect.
In short at least in a couple of cases microbiome effect has been shown to be the cause, but it is difficult to speculate how far this can be extrapolated. Second, There is a huge set of examples of microbes countering the strength of other which is an important ability of residential flora. I projected that having a more diverse population will be self controlling and more balanced. On the other hand, if the diversity is effected allowing some strains to predominate which may in-turn influence the normal process to a higher degree tipping of the balance. This hypothesis allows variability of the microbiome to be accounted for.
I have posted thoughts in my blog. http://varuncnmicro.blogspot.in/2015/03/a-thought-on-microbiome.html. Wonder what TWiM host's think about this.
In TWiM 100, the discussion of how a single mutation can make the difference was great. I felt you should have mentioned the Small things considered blog with same theme.
Evolution of a Superpathogen. http://schaechter.asmblog.org/schaechter/2015/03/evolution-of-a-superpathogen.html
I couldn't shorten the mail further. I wanted to say it all. As always, You guys are great.. Keep the science shows coming.
Varun C N
Matt Daugherty writes:
I just listened to the latest TWiM. Thanks for covering our horizontal gene transfer paper! It was great to hear you all talk about it and give your thoughts.
With regards to the selective pressure for retention of the Dae’s in genomes once the extremely unlikely horizontal gene transfer event happened, I’m not sure we will ever know the bacteria that drove that. For instance, in ticks and mites, it was likely an ancient pathogen of that ancestral chelicerate over 400 million years ago. Borrelia is a current bacteria in one lineage of ticks, but is not in other mite and tick species (to my knowledge), so while the Dae2 gene works against Borrelia in the deer tick, we have to infer that it also works against several other bacteria in these critters. Finding out what those bacteria are and how inhibition of their growth would have driven retention of Dae’s is, of course, an active area of study now that we know these antibacterial genes exist in these species.
Hope all is well there.
Perhaps it has already been brought up but, in your discussion of the shipworm / bacterial symbiosis, you didn't mention a, to me, rather remarkable point: This symbiosis involves anaerobic bacteria on the gills, the very point of maximum oxygen saturation (I presume) in the shipworm's body! I would have to suspect that the symbiotic trade-off, at least in part, would have to involve enzymes for shelter from oxygen.
Dear Wonder TWiMs,
I just listened to your discussion of nitrogen fixation on TWiM 94 and greatly enjoyed it! My current research is on Azotobacter vinelandii and its nitrogenases, so nitrogen fixation is close to my heart (and mind) right now. I hadn't heard about these algal symbioses before though.
A couple things I would add, for general interest:
Nitrogenase as an enzyme is good for reducing N2, but it can also reduce a lot of other similar-shaped molecules! Acetylene (C2H2) is one, commonly used in assays for nitrogenase activity, but the enzyme (at least, some forms of it) (and in vitro at least) can also act on carbon monoxide, cyanide, and even carbon dioxide, reducing them to mainly hydrocarbons. So this could be an ancient link between carbon and nitrogen cycles. A hypothesis, anyway.
Despite the toxicity of oxygen, Azotobacter is an obligate aerobe, with very high rates of respiration observed. It's been thought that this high respiration rate is part of what protects the nitrogenase from oxygen (reduce quickly O2 to H2O before it can react with the enzyme). My reading so far suggests this is controversial though.
Thanks for all the good discussions,
I thought you and the rest of the TWiM/TWiP folks would be interested in the following paper: Transferred interbacterial antagonism genes augment eukaryotic innate immune function, published online in Nature this week. Matt Daugherty (Malik Lab) who you know, co-authored the paper with Seemay Chou (Mougous Lab). We've had a lot of fun following this story in the lab. I think it's a beautiful example of interdisciplinary approaches coming together to uncover a very cool bit of biology.
Happy Holidays to the entire TWi-fecta,
Dear Mr. Pres., Pres alum, and Pres to be,
Elio said Cretaceous referring to four hundred million years ago and Michael agreed. I thought, wait! That's when Jurassic Park was set (Cretaceous), ie in the last era of the dinosaurs (exclusive of birds), from one hundred some to sixty six million years ago. You guys were talking about how ancient must be the tenuous association of the tiny cyanobacterium with the tiny algal bit in getting fixed nitrogen into the eukaryote.
Four hundred million years ago was just at the end of the Devonian and beginning of the Carboniferous. I had to look that up.
Perhaps you meant the era starting with a "C" which was not the Cretaceous.
Looking forward to contemplating my metabolibiome under the influence of my Microbiome and my virome, enjoying my insomniac listening again,
I remain faithfully yours,
For those unacquainted with the Armed Forces, about the email question on food safety:
Hello all, Thank you for for the wonderful and insightful podcast. I am a somewhat regular listener as I work in viticulture and spend my spring summer and fall scouting vineyards advising grape growers on integrated pest management in Northern California. It was brought to my attention by my girlfriend and dentist that new born children are born with sterile mouths. I am curious as to why this is the case? Could it be that some newborns have colonies of bacteria that are passed on from the mother?
Thanks for your thoughts on this question. Happy New Year!
Just found an interesting paper suggesting the microbiome of the placenta...
Greetings. I have just finished episode 77, so I am slowly catching up. I wanted to say that while I am a layperson as an elementary school teacher and hobbyist fermenter, I enjoy learning about microbiology and find the topics fascinating on the show. One of the anthropological aspects of food that I find fascinating is and other foods where saliva has started fermentation although I would hesitate to try this myself.
I wonder how much this kind of thing impacts the diversity or monotony of the indigenous population's salivary flora.
Overall, I just wanted to say thanks for a good show and I look forward to getting caught up soon.
Bethany, Austin Tx
A question from TWiV (Caroline)
Are virus infections more likely to be species specific than bacterial infections? It seems to me they would be since viruses rely so much on the specialized relationship with cells for "survival".
Hi guys. Sorry for such lag in response. Re: number of rats in NY -- I'm uncertain. Heard a couple million recently. However, I felt obligated to share an anecdote. Popular Canadian life scientist David Suzuki in interview with Bill Moyers a few years ago stated, sharing an air of astonishment and awe, that planet earth now has more humans than it has rats. This is noteworthy, of course, because rats are so much smaller, eat so opportunistically, and reproduce so florescently, that you'd kind of think there'd be more of them than of us, overall. There must once have been. That was his impression, anyhow, and I was willing to buy in. It sort of left an impression of the massive quality of earth's infestation with H sapiens at this point. Just think.
Next time, I've decided to share with you the story of the remarkable biofilm I've been able to cultivate in my, at this stage, really dramatically bachelorized toilet. I'm obligated to be embarrassed, and unequipped to analyze it, but it really seems pretty astonishing. I hope to spell it out for you in a message to follow, as long as you assure me of some modesty in revealing the attribution.
One time, I may tell you about the bioluminescent, presumably fungal, growth observed in my compost heap while turning the thing in the dark of the less hot night a while back.
No more rain here. Cool weather, finally, but no exceptional freeze, and probably warmer average. No rain and some sunshine cooks ozone and nitrogen oxides, irritating the lungs of many worse than in most places. We have particulates too, of course, which are pleasantly washed away for a day or two by some rain. Do expect not very pleasant.
PS heaps of praise on your communications works. - d
A paper just published in nature:
reports an effective antibiotic against world class killer bacteria including tuberculosis, MRSA and C. diff. Is it too early for a TWIM on this? Would be interested in so many aspects including whether anyone has found the bacterium responsible and what the chip does for "in vivo situ" detection in the dirt where the "unculivatable" bacteria live.
Was 21C this afternoon and sunny although a cooling trend is forecast.
Wow, what a wonderful world it can be,
Hi Dr. Vincent and the TWIMtastics,
Thanks so much for your V101 course! In lecture 5 and the slide on estimated speeds of viruses through the cytoplasm, I was struck by the difference between the velocity of the bacteria Listeria Monocytogenes (LM) with its Actin tails in cytoplasm versus these more sedate diffusion times. Given gene sharing, I wonder why more bacteria haven't been discovered using that mechanism. I learned of LM from Michele's discussion of Dr. Portnoy's Listeria work in TWIM #79. It is so fascinating and possibly world health changing. Perhaps Dr. Portnoy could be invited to do a TWIM. There are at least two helpful youtube videos:
The first is 16 seconds long and shows LM racing around a cell and creating protuberances in order to be phagocytosed by an adjacent cell. It's a favorite of mine and is called "Listeria monocytogenes" by Jun S:
The other is a 43 minute presentation by Dr. Portnoy describing some of his work called "Listeria: From Food Poisoning to Cancer Immunotherapy":
Michele might have already posted one or both of these.
Thanks so much. You have set an example to which all podcasters should strive and a model that many would do well to adopt. Oh, 14 degrees C here and light rain which we really need. Hoping the Northeast can dig out from it's record snowfall!
Re: the letter which was under discussion when I came into TWIM just now, in the last few minutes of the episode:
The sensitive science fiction author Clifford D. Simak published a story fifty-some years ago, about a peaceful society and how it happened that they could be that way. Every so many generations they would go ask ceremonial questions of the omniscient computer, after carrying on life as usual for a goodly time.
First question was, "What is the purpose of the universe?" Answer: "The universe has no purpose. It just is."
Second question was, "What is the meaning of life?" Answer: "Life has no meaning. It is an accident on the face of the universe."
After that everybody could go home, go to the rocking chairs on the porch and resume shucking the peas while telling each other entertaining stories about life, the universe, and everything. Certainly nothing to fight about, given sustainable resources.
Unseasonably hot October in Fresno. No rain.
PS Now that the show's over today on Science360 internet radio, I'm gonna have to go get the podcast for myself. I'm lazy, and prefer to have a DJ bring it to me, while I'm shucking the peas. d
he added later:
Y'know, I think the two questions make more sense the other way around. I got it backwards.
1) Meaning: Life is an accident.
2) Purpose: The universe just is.
In light of the discussion about C. elegans in TWIM 89 have any of you seen the OpenWorm? I just ran across it. Jim, Smithfield, VA
As a mostly bed-bound sick person, I really must thank you and all your team at TWiX for helping me to keep my sanity with your wonderfully absorbing and entertaining podcasts. With your frequent asides into seemingly almost any subject under the Sun and out into the depths of the Universe, distant past, present and, speculated, future, you keep my mind as active as it could be, and it helps me feel a part of the real World, away from the confines of my room. I'm even beginning to form a mental map of the USA, its wildlife, and even weather, which is something I've always felt I needed to study more.
I loved the idea of the 'nitrochondrion', and will need a few more listens through to take it all in, but I think I ought to ask you and Elio to clarify at least a couple of 'conversational typos', for the benefit of other listeners:
I'm sure that many people will have written to you about the assertion that the *Cretaceous* (Carboniferous) Period was 400mya; but some may not notice the conflation of water fern and duckweed. Elio did say, correctly, that Azolla was a fern, but this was after he already said it was duckweed. He clearly knows it isn't, but the listeners may not all appreciate that.
Azolla is a serious invasive alien plant in UK wetland habitats, and can quickly choke out almost everything else when it gets into ponds where there is nothing that can control it or compete with it. Even the duckweeds that might, otherwise, cover the whole surface of ponds, can be deprived of the open water that they need and be replaced with an almost hummocky surface of piled up water fern. It can be quite a dismaying sight to go to visit a pond from one's memory, and then see, as one approaches, where it used to be, the tell tale red of the hummocky surface of water fern that has obliterated it.
I don't know if anyone has yet come up with a safe and practical control method. I used to get a bit concerned when eutrophication had enabled the duckweeds to cover the whole water surface, but this Azolla, is orders of magnitude worse.
These slips and 'typos' are inevitable with such a wide ranging and unscripted format. In a way, they are the 'deliberate' 'Where's Wally's' that encourage us to keep listening carefully.
May they, and you all, long continue.
Best wishes for the New Year,
(Wet and windy with a high of 3C)