Real-time Evolution

I don’t usually take a lot of this space to talk about work-like things.  But today, I came across a scientific paper that was just published that has nothing whatsoever to do with what I do on a day to day basis, but is just so damn cool, that I wanted to bring it to people’s attention.

The researchers followed a patient that had a Staph aureus infection from its early stages until it developed resistance to the antibiotic vancomycin (about three months).  At different times they took some of the patient’s blood and isolated the bacteria in it.

DNA

Each time they isolated the bacteria, they sequenced its DNA.  All of it.  The whole genome.  Each time.  2.8 million bases per experiment.  They did this 9 times over three months – which is astounding as I think back to being a grad student (circa 1991) when sequencing DNA by hand I was happy to get ~300 bases in a good experiment that took me a full day to do.

 

Even cooler than the technical achievement of new sequencing processes, the researchers were able to see 35 different mutations grow into the bacterial population sequentially.  These new mutations correlated with increased resistance of the Staph aureus to the antibiotic.

Observing selective pressure and responsive evolution in real-time – absolutely amazing.

When sometimes doing science for a living seems like job, its stuff like this that really helps restore the joy and wonder of it.

Read and post comments |
Send to a friend

24 thoughts on “Real-time Evolution

  1. That's really cool. I wonder if these mutations are in any way racing against the human race's methods of wiping them out. In other words, if humans never existed, would the mutations be different or less "virulent"? (No pun intended).

  2. in my previous life as a biology student, i used to LOVE DNA sequencing. not that our experiments were usually very complicated, but there was something so rewarding in working all afternoon to get the gels *just right* and then zaaaapppppppp the electric current created all these beautifully positioned stripes.ah, the days when i would pretend to be all sciency and smart. now i'm all wordy and smart. teehee. :)

  3. Damn you making me want to get into biological research! I'm an engineering major so it'd be hard, having to take lots of bio classes to "catch up" with the others. *sigh*

  4. Here's how I know I'm not a scientist. After I read "sequenced its DNA", I don't remember reading anything else until I got to the last line. And this is what my husband does for a living for goodness sake!

  5. This is very strange. I just read a chapter about sequencing DNA genomes in The Time Traveler's Wife and then closed the book to check Vox. It literally talked about how amazing it is to sequence the entire genome. Coincidences are so bizarre sometimes. Also, although I'm sure everything you wrote about is very interesting, I'm very glad I was an English major. Like HannahBanana, everything went right over my head. :)

  6. I'm a science nut and i want to thank you for sharing. there is
    so much we do not know…I'm lcurrently learning about
    GLYCONUTRIENTS..does anyone else know anything about them? they
    use to think there were these arm like structures coming off of each
    cell to help it communicate with all the other cells in the
    body…recently they discovered there are fingers on the ends of the
    arms ( of sorts) that need to be there for 100% communication.
    What I have learned is that the American diet only contains 3 of the 8
    GLYCONUTRIENTS…so our bodies cells are NOT communicating at 100%..no
    wonder we're sick…a cancer cell develops and if the communication is
    not there between cells it bumps into it and says "have a nice day"
    instead of saying "OMG alert alert we have a problem here..we need to
    EAT these cancer cells". It's facinating science.

    YOU can get GLYCONUTIENTS by eating AS FRESH AS YOU CAN GET
    veggies! So EAT IN your garden..right off the vine..as soon as
    you pick a veggie or fruit the life force begins to die..even if it is
    ORGANIC…don't think that organic is much more NUTRIENT RICH than
    regular old NON-organic food…it's not…it just doesn't have the
    chemicals with it….So GROW those gardens this year folks…it's not
    too late to start…and reap the benefits of glyconutrients the natural
    way…do your own research too..it's facinating :-)

    Thanks for sharing:-)

  7. Maya — you're absolutely right — these mutations "blossomed" because of the selective pressure of the anti-biotic. If the anti-biotic wasn't there, those mutations would have occurred at a normal rate, but there would have been no advantage for them in the general population. Of couse, the "regular" S aureus is deadly enough to kill you, so talk about a no-win situation.
    We're really in an arms-race against these guys, and their generational cycle is so fast, its hard to make new antibiotics to defeat them.

  8. Angelanoel — don't think because you're an engineer that you can't impact the life sciences — the Human Genome Project was a huge success — ahead of schedule and under-budget — because scientists, engineers, statisticians, materials scientists, etc. all worked together on doing something that 10 years before had been unthinkable.
    I really think all the great-leaps-forward in this century are going to be b/c people from different disciplines get together and make things happen.

  9. so what's in our future 10 years from now? can our immune systems keep
    up or are we in for some "super immune" systems for the future?
    do we really think that bacteria and strains like this one are not
    smart enough ( servival of the fittest) to outrun anything we would
    concocked to kill them? and have we thought about the idea that
    maybe we NEED these bacteria so that we can survive something coming in
    the future? why is it human nature to kill anything that doesn't
    seem to have a purpose on the surface and get rid of anything
    that causes pain? pain is one way the body tells us something is
    wrong…if we have no pain we don't know something is "wrong"…

    this post got me thinking this morning.. just rambling…
    ~Amy~

  10. Great post Steve. As always…Science RulesAmy- "why is it human nature to kill anything that doesn't
    seem to have a purpose on the surface and get rid of anything
    that causes pain?" I don't think this is at all what anyone is trying to do. I doubt you could find a scientist that wouldn't tell you that without bacteria we would be in serious trouble. Staph, like all bacteria is fine in small numbers but deadly in large numbers, which is the only time we need to kill them. Research like this is aimed at treating INFECTIONS, not wiping out all Staph on the planet, as if we were even close to that possibility to begin with.Glyconutrients is a term invented by supplement vendors!!!!! We have evolved the ability to inter convert all these sugars that they are claiming we need to supplement. There are no reliable, controlled studies to show that glyconutrients provide any improvement against any medical disorder.

  11. sdede2..I was meaning people in general..not scientists per say…most
    people want pain to go away..most people want to kill anything that
    they "think" is bad…all I was trying to say was that we have to look
    deeper..everything in my opinion has a reason for being here…the
    good, the bad and the ugly.

    As far as glyconutrients go…I have my own story as to how they have
    changed my health drastically…I believe what they do in my body is
    balance and align the communication between cells. There is a
    whole University now in England , built and dedicated to studying these
    sugars. It's NEW science…not to say that there is not always someone
    out to make a "buck"…it's business..it's what America was built on
    right? being your own boss? small business owners….I respect
    your opinion and your view point, however it is not my own…everyone
    needs to make up their own minds…not all things work in all
    bodies…thank goodness we have a choice still in the United
    States…so that we can find what works best for each of us.

    Thank you for sharing your view point with me.

  12. Amy — Sdede2 is correct. "Glyconutrients" has been coined by alternative-medicine advocates as one of the latest trends in "nutriceuticals". Nearly all proteins you eat are glycosylated in some way — and gastro-enteric metabolism doesn't allow the ingestion of intact proteins whole anyway — they are broken down into their basic components (catabolism) and re-assembled as needed or used for fuel — we can synthesize all the carbohydrate monomers and polymers that we require.
    A search of the NIH database of scientific literature (PubMed) shows no peer-reviewed papers on glyconutrients and certainly no clinical evidence. Caveat emptor.
    That said, I couldn't agree more with you call for eating more fresh vegetables. There are a number of vitamins in vegetables (which our bodies DO absorb directly and use) that are degraded over time as a picked-vegetable ages. So the fresher, the better!

  13. Amy- I hope I didn't sound too harsh earlier because I didn't mean it at all that way. I respect your wanting to inform yourself instead of believing anything you hear. I often hear people make statements just like yours or very similar. "If it makes sense to me I'll try it","Not all things work in all bodies". The problem here is that without a good science foundation I can convince you that water should be a banned substance! Trust me I've done it many times. ****off topic*****Everything written below is 100% true!Di-hydrogen monoxide causes thousands of burns a year in it's gas form, as a liquid it kills hundreds every year worldwide, in it's solid form it can cause drivers of cars to loose control of their vehicle. This substance surely must be banned immediately right!!This is a simplified example that could go on and on until your convinced. The answer is simply steam burns, drownings and ice on roads and you've just convinced someone that water should be a banned substance. **** OK back on topic*****Terms like balance and align the communication between cells are HUGE red flags that what you are being told is quackery. Also when people claim something is NEW science it's usually because what they are claiming is not supported by the hundreds of years of "old" science that we have based our entire society on. Things that we know are true like the absorption of peptides not intact proteins! I completely agree with Steve, the fresh veggies are best for vitamin content and the fresher the better. That's true for taste too as far as that goes in my book. I can't wait to get at some Michigan Corn and Apples…:)

  14. Thanks for helping me see my life more clearly.
    IF we are to eat more veggies…how do we know that what we're
    eating is "safe" and actually has all the NUTRIENTS in it that the
    "government" says are in it?
    ( I wish I could do my own tests in my cellar because I would lol)

    I know a lot of people who say that taking a pill is safer in a
    sense than eating vegetables from the store because you know nothing
    about where those vegetables actually came from( we know what we're
    told, but how do we know we can trust it?)…where as with a suppliment
    company, like Shakee, for example..because they do actually have
    independent clinical studies to back up what's in their products, you
    are assured of what you're putting in your body.

    This is what I hate about this world…I just want to be told THE
    TRUTH..whatever that is lol…so I can make an informed choice. I'm
    smart enough to do that!

    OK so….with your example of water…I get that :-)
    Let me ask you and Steve…because this is always a drop in the
    POSITIVE bucket for me…what do you do personally? how do you take
    care of your physical body each and every day? ( I'm probably
    secretly looking for MORE motivation here for myself..yeah I know it's
    selfish but it's ok in my book LOL)
    I didn't have any soda yesterday…first day in years…today I aim to
    make it another soda free day ;-) I know silly maybe compared to
    some..but huge for me ;-)

    My SECRET goal, and don't go tell my doctor this, is to heal my body
    enough that my thyroid wakes back up and starts working on it's own
    again and I can get off the armour. Is it possible? YES!
    with my family history based in chiropractic ( went to school to become
    one)…I have been taught my whole life that when the body is given
    what it needs it can and will heal itself. I guess I'm in the process
    of finding what works for me. :-)

    My goal in this life is to become as healthy as I can be through natural means.
    When the doctor told me that i would be on thyroid meds the rest of my
    life I about DIED! Literally…part of the reason for the Coyote Bones
    Cafe is due to my need to get healthy. ( The Cafe will be organic as
    much as possible.) I personally want a place to go to feed my bodyand
    spirit…not fastfood not eating out at some restaurant where the food
    is old but they make it taste good LOL :-(
    No LIFE FORCE left in it at all. I am a food addict…my choice of food
    has been fastfood for a good 15 years…I know what I've done is NOT
    GOOD…working through emotions..and not eating my feelings all the
    time will make the biggest changes :-)

    So any suggestions to add to my life style change? from anyone? I'm open lol.

    Life is good today and i trust you all have a wonderfully happy and safe holiday. Go have some fun!
    ~Amy~

  15. WOW great post Amy.Not sure I can cover everything you mentioned but will comment on a couple of them.The idea that your body can heal itself if "allowed" to is simply incorrect. It is even controversial amongst chiropractors that I have heard speak. I hear this belief often with the kidney patients that I work with. They believe that they will heal themselves and come off dialysis someday. I hear this based on diet beliefs, religious beliefs and simply "resting" their kidneys. The number of people in my career that have actually gotten to come off dialysis after a diagnosis of chronic kidney disease is VERY small, less than 1 percent.Now I feel that people can believe what ever they want. My fear is however that they are damaging themselves through avoiding treatments that can truly help them live longer, but because of misinformation they are avoiding them.Life Force? How is this measured, or quantified, or even defined? You could call it anything? If the lack of Life Force means high fat, saturated fat, high sodium, high simple sugars, like the fast food you mentioned; I think that term has already been coined…Junk Food!!!…:) :) I think the idea of an organic minded restaurant is brilliant and if there was one in my town I'd go there often.Now the other stuff you mentioned about food. The nutrient amounts that you can look up for corn for example are just averages. Not every kernel of corn is equal…:) That being said, if a plant doesn't have the nutrients it needs to grow properly, it simply won't grow, or will have under developed fruit (which is what corn is) etc. You can therefore be pretty certain that a cup of corn will be close to the nutrient amounts as averaged. This is why, as the American Dietetic Association has always said, eating a variety of foods everyday with a combination of 5 fruits and vegs is the best thing to do. Also you can of course always question anything to the point of ridiculousness, this information is pretty trustworthy however because as in any science is it must be repeatable, over and over the same results must occur. Oh one more thing on that. The idea of a huge conspiracy that every scientist in the world is a part of, as many people claim, is also so ridiculous it boggles my mind. Steve could reply more to this than I could I'm sure, since he would actually have to be part of the conspiracy…:)Personally it's 10:00 AM here and I've eaten 2 pieces of fruit today already, a banana and an apple, and I'm eying that pear as lunch is still 2 hours away.HeHeHe…

  16. thanks for your response…
    I believe I have to do whatever is in my power ( and everyone is
    different) to stay healthy and live a LONG and PRODUCTIVE life…when I
    said our bodies can heal themselves I didn't mean that you can just sit
    around and "wish" for it to happen.
    Just wanted to clear that up. LOL I believe I have to exercise (
    a lot) if I want to lose weight because I already have one strike
    against me ( hypothyroid disease) but even as I type that out..if I
    truely believe in the Law Of Attraction..I need to start looking at it
    differently. I do believe in MIND over MATTER BUT…to a certain
    degree only…it must be combined with the body and spirit as well~ to
    be healthy, whole, happy, and "balanced".

    SO what can I do…what is in my power to do TODAY to exact the changes I seek?

    I am right with you when you say people are hurting themselves by not
    taking advantage of everything out there to heal themselevs…but don't
    you think that part of that has to do with the media, education and
    cases where people go into the hospital to have a biopsy on a lung and
    end up having there spleen removed because someone didn't do their job
    correctly? ( speaking "generally" here of mis-trust of the medical
    profession)…and you did say "misinformation" ;-)

    Anywho…just trying to figure out my life :-)
    Thanks for the back and forth :-)
    have a great day and YES eat the pear!
    ~Amy~

  17. I completely agree about the hospital thing. It's like our society perpetuates the idea that when you are talking to your doctor you can just turn your brain off and do whatever they say and its correct. Its a tough thing to do I admit. I think you have to listen to what your physician is telling you, understand it as completely as you can and then make decisions for your own well being. One problem that usually arises (from my experience) is the fact that people don't want to learn from their physicians/dietitian/nurse practitioner, they just want them to tell them what to do. As a dietitian I constantly get asked by patients "Is it OK for me to eat that?" This is a very complex question that always has the same answer–"It depends" Some things are almost always OK for them to eat while others are almost never OK for them to eat and then there is everything in between. So to be able to answer that question someone has to understand their disease process and diet enough to make that decision. This is not what people want though. It's amazing!! What they want is a LIST of things that they can always eat and a LIST of things they can never eat, so that they can shut their brain off and not have to think. It drives me up the wall!!!I hear what you are saying about the healing yourself thing and I agree with most of what you say…:) I agree that exercise could be looked at as healing yourself. In fact my step-mother, who is a physician at U of Minnesota hospital uses the term "EXERCISE IS MEDICINE" on her patients all the time and I love that!! I also agree that eating healthier can be looked at in the same way. However, things like an infection ( I think that was where this discussion started…:) that's so funny) often cannot be healed by your body alone and require antibiotics. These antibiotics need to be used when "good" bacteria get out of control as much as when "bad" bacteria get introduced where they are not supposed to be.FYI: I ate the pear…:)Scott

  18. Pingback: Religion Drives Evolution | Stevil

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s