I’m glad the Large Hadron Collider is getting so much press; it’s a rare day that physics takes center stage in the minds of everyday people. Searching for fundamental unifying forces of the universe by smashing atomic particles at near-light speed into each other inside the largest machine ever constructed by human beings is pretty damn awesome. The cutting-edge discoveries that come from it (or the ones that conspicuously fail to) will undoubtedly play a large role in our understanding of the most illusive workings of the universe. So you might be surprised to know that I find research that began 20 years ago with some bacteria in a jar to be even more exciting.

Richard Lenski’s research at Michigan State University is breathtaking. The procedure is stupefyingly simple but the results are stunningly elegant. Not only has he observed evolution in a laboratory setting, but he’s provided snapshots of every step along the way. And when a novel ability was eventually coughed up by natural selection, he rebooted from past generations to see exactly where and how it happened.

It all went a little something like this:

In 1988 Lenski and his team started out with a single microbe of E. Coli, allowed it to divide, and from its offspring he started 12 colonies. They were kept in separate containers, each filled with a glucose-citrate solution. Every day, samples from each colony were frozen and the solution replenished. (E. Coli feed on glucose, but it is an identifying attribute of the bacteria that they can not consume citrate because they are unable to pull it through their membranes.) This process provides a record of genetic change every 500 or so generations that can be resurrected and compared to bacteria at any other stage.

From Carl Zimmer’s article A New Step in Evolution:

Over the generations, in fits and starts, the bacteria did indeed evolve into faster breeders. The bacteria in the flasks today breed 75% faster on average than their original ancestor. Lenski and his colleagues have pinpointed some of the genes that have evolved along the way; in some cases, for example, the same gene has changed in almost every line, but it has mutated in a different spot in each case. Lenski and his colleagues have also shown how natural selection has demanded trade-offs from the bacteria; while they grow faster on a meager diet of glucose, they’ve gotten worse at feeding on some other kinds of sugars.

But then… after 33,127 something weird was going on.

The flasks can sometimes get cloudy as a result of foreign citrate-eating bacteria invading accidentally and thriving. When this happened, Lenski and his team would just throw out the contaminated specimen and reboot from the most recent unadulterated version. In one case however, it wasn’t infiltrating alien microbes. The E. Coli had gone through several mutations that allowed it to feast upon the hitherto-unmolested citrate, a feature that has only been seen naturally in E. Coli that has transplanted DNA (in the “wild” E. Coli can sometimes exchange bits of genetic code with other bacteria). These guys evolved citrate-consumption all on their own.

Again from Carl Zimmer:

Blount took on the job of figuring out what happened. He first tried to figure out when it happened. He went back through the ancestral stocks to see if they included any citrate-eaters. For the first 31,000 generations, he could find none. Then, in generation 31,500, they made up 0.5% of the population. Their population rose to 19% in the next 1000 generations, but then they nearly vanished at generation 33,000. But in the next 120 generations or so, the citrate-eaters went berserk, coming to dominate the population.

This rise and fall and rise suggests that the evolution of citrate-eating was not a one-mutation affair. The first mutation (or mutations) allowed the bacteria to eat citrate, but they were outcompeted by some glucose-eating mutants that still had the upper hand. Only after they mutated further did their citrate-eating become a recipe for success.

For more of the technical (read “awesome”) side of things, read the rest of Zimmer’s article, Lenski’s Experimental Evolution website at MSU, and the paper abstract (abstract is jargon for a research paper’s summary and conclusion).

If you’re still wondering to yourself “How on Earth can this guy be more interested in E. Coli evolving than exploding protons generating microscopic black holes that dissipate instantaneously?” then well, you might have a point. I understand how that would be more appealing to some, but when you view this research in the context of all that evolution informs us of it is profoundly exciting.

Every single one of us shares a common ancestor. On top of that, we all share a common ancestor with E. Coli and the only thing that separates us is millions of years of the exact same process that has been observed and documented by Lenski and his colleagues. If that thought doesn’t turn your brain into a mushy pile of awe-goo I don’t know what will.

Prepare yourselves, for below the fold lies the startling secret behind the mysterious phenomenon known as Crop Circles…

via Skepchick

I’ve been following the LHC project for quite some time now and I was really excited about it starting up yesterday. It’s been getting lots of press in the last few days regarding the crackpots who think it’s going to result in a black hole and destroy the world. Obviously, this hasn’t happened, but it seems it’s all the media care to focus on when talking about it. Never mind the possibility of actually finding the Higgs Boson and unifying fundamental physics. My frustration with the apocalyptic stylings of the media has just hit critical mass thanks to this:

Phil Plait over at BadAstronomy brings to our attention an Indian girl who killed herself out of fear of the LHC. Apparently the Indian media has really blown this one up and coupled with their heavily superstitious culture has created a bit of a panic over there. Plait doesn’t play the blame game though, placing responsibility squarely on us and really hammers home the need for critical thinking:

All over the world, in all different countries, people are raised to believe in superstitious nonsense, and raised to believe with all their hearts that it’s real.

And when we do that, we do far more than remove people from reality. We leave them vulnerable to all manners of nonsense, from believing in fairies to truly and honestly thinking the LHC will destroy the planet. People don’t learn how to think critically, and then they drink homeopathic water instead of taking real medicine, they chelate their children, or they deny their children vaccinations. And when that happens, people die. Children die.

I’m a parent. I sometimes think the most important thing I can do for my daughter is love her, keep her healthy, protect her. But in all of those, there is an overarching responsibility for me to teach her how to live in the real world. And that means showing her how to think. Not what to think, but how

Most people don’t see critical thinking as an important faculty in daily life, or they consider their “common sense” to be adequate. Stories like this make it very clear that that isn’t the case. “Common sense” just isn’t enough. All beliefs, superstitious or otherwise, must be continually examined and updated to reflect reality as best as possible. Critical thinking is critical in every sense, and relinquishing it would be to doom us in a way untouchable by any mere partical accelerator.

Amidst my frantic assembling of necessities for my third (and final) year of collegiate education, I’ve been catching up on my myriad of awesome podcasts. Another great one for your consideration is Atheists Talk, produced on AM 950 by Minnesota Atheists. They do a great show and have had the likes of PZ Myers and Lori Lipman Brown of the Secular Coalition of America among their guests.

This past week’s show is titled All About Humanism and is an excellent primer for anyone interested in the subject. They take questions from a live audience (this broadcast was hosted at the Minnesota state fair) and go over the key points of the Humanist Manifesto, a wonderful document that begins thus:

Humanism is a progressive philosophy of life that, without supernaturalism, affirms our ability and responsibility to lead ethical lives of personal fulfillment that aspire to the greater good of humanity.

The lifestance of Humanism—guided by reason, inspired by compassion, and informed by experience—encourages us to live life well and fully. It evolved through the ages and continues to develop through the efforts of thoughtful people who recognize that values and ideals, however carefully wrought, are subject to change as our knowledge and understandings advance.

It’s hard apparently easier than you’d think to imagine how anyone could disagree.

If you’ve never heard of the podcast Skeptoid, you’re really missing out. Imagine Penn & Teller: Bullshit! minus profanity (and with some regret, nudity), about 10 minutes long, and produced weekly without breaks. Brian Dunning does a masterful job bringing everyday skepticism to your ears.

His most recent podcast is titled How to Be a Skeptic and Still Have Friends, a bit of a divergence from the usual debunkery, but very well worth listening to. My closest friends are almost all skeptics, though some might not use the word or aren’t familiar with the movement. However regarding day-to-day interaction with other people I found this podcast to be very insightful.

Focus on where you agree, never on where you disagree. Start by finding common ground. No matter who you’re talking to, they have some level of skepticism about something. Ask them, “Isn’t there some myth you’ve heard that you don’t necessarily believe?”

They’ll answer “Well sure, Bigfoot, space aliens,” whatever.

Tell them “I’m skeptical of Bigfoot for the exact same reasons you are. Tell me why you don’t believe in Bigfoot?” And now you’ve got your friend telling you the very reasons you’re skeptical of the new claim. The evidence is of poor quality, it’s too improbable, whatever it is. Help your friend along. Point out more reasons to be skeptical of Bigfoot. Be familiar with our checklist of 15 warning signs to help you spot pseudoscience from Skeptoid episode 37.

And then, once you have a good list, apply that same reasoning to the new claim. “We agree that part of the reason Bigfoot is suspect is that we have low quality evidence coming from people with dubious credentials. We can also find those same problems with the claim that you can run your car on water. Also, we agree that one reason Bigfoot is improbable is that if it was real, we’d have known about it by now — people have been living in Bigfoot habitat for hundreds of years. We can say that same thing about running your car on water — science has known all about oxyhydrogen and electrolysis for hundreds of years and exploited it many different ways. It wouldn’t have to wait for some guy on the Internet to claim to know something that science doesn’t.”

While checking my facebook page, I saw that I had a new friend request. I clicked through to the page to view the request and saw this:

I imagine they found me through one of the various science/atheist/secular/skeptical groups I belong to. It seemed a strange way to recruit and the image an odd choice for a personal profile. My skepticism was mildly aroused as it seemed almost a charicature of science-enthusiasts. So out of curiosity I copied and pasted the link to check out the group. Not at all surprisingly, this was the result:

Honestly, I almost can’t bring myself to believe they sincerely think this would convert anyone. Maybe they’re just out to annoy. “Yeah! This’ll show those hethens!”

In response to this blog’s creation, a friend of mine queried thus:

what actually convinced you that there isnt such a thing as “god” anyways?

i just don’t see any sufficient evidence for either side anymore, and i want to know how you can call yourself an “athiest” when i can’t leave the viewpoint of an “agnostic”.

i wish i could believe in a “god” like i used to, however i’ve grown too much in the past four years… from someone with blind faith to someone too logical to even know how i feel about the word “faith”.

This is a legitimate question that a lot of agnostics pose and I’m glad she brought it up because I feel it’s worth addressing. First off, I’d like to define Atheism.

Atheist

–noun a person who denies or disbelieves the existence of a supreme being or beings. (emphasis added)

Many people forget that atheism can mean both active denial or a simple lack of belief. In this second sense, agnostics can also be accurately described as atheists. So to be clear, there is no way to disprove the existence of a supernatural being, making me in the strictest way, an agnostic. I choose to identify as atheist because while we may never be able to say conclusively one way or the other, that does not mean that both are equally probable propositions.

There is no way, in principle, to unequivocally disprove the existence of countless things. We must all be, strictly speaking, agnostic about invisible unicorns, faeries, flying spaghetti monsters and celestial teapots, but we do not take the inability to disprove these things to mean that they are as equally probable to exist as to be fabrications of our human imaginations.

So on a scale from 1 to 10, 1 being 100% sure of the existence of a deity and 10 being 100% sure of the nonexistence of anything “supernatural” I must firmly remain a 9.999. I am a naturalist who sees no evidence for any kind of intervening being, benevolent or otherwise. With our present understanding of the universe, the only room for a “creator” is in gaps of knowledge with regard to the “beginning” of the universe, but I find that kind of deism to be wholly unfounded and intellectually dishonest to the methods of science.

On a final note, I would like to add that “atheist” is not my favorite way to describe myself. It’s useful if I don’t have time to engage in a productive conversation because it quickly establishes my position in the minds of most people. However in an ideal situation I much prefer to identify with more positive terms, rather than to be defined in opposition or lacking of something. Humanist, naturalist, secularist, and non-theist are more descriptive and the first three describe active beliefs and morals instead of just describing the beliefs that I lack.

So just a quick update on the last post before I put up something new.

My friend had Dengue Fever, also known as bonecrusher disease. She is now out of the hospital and doing much better.

One of my best friends is currently in the hospital with an as-yet unknown ailment she picked up during a trip to Argentina.

Neither of us are religious, despite both of our families and many friends belonging to our old church. So when just about everyone who visited or called assured her that “I’ll pray for you” I had some very mixed feelings.

At first I did what I always do when someone mentions religion around me and her, I shot her a sarcastic look, which she reciprocates. It’s usually like in Fight Club when members give each other a little nod when they meet in the outside world, except this time it seemed like it really bothered her. I realized she must be getting that all the time being in the hospital and the fake smile you give a person who says it probably gets really tiresome. I was mildly outraged that people would be so insensitive to another person’s worldview.

Of course most people who “send their prayers” don’t really think about it that way. For them it’s assumed that it’s doing practical good for the recipient and because they surround themselves with like-minded religious people it doesn’t ever occur to them that it might be insensitive. It’s like the “Merry Christmas” vs “Happy Holidays” debate. People who regularly say “Merry Christmas” think nothing of it, and assume that everyone understands it as a polite gesture. But how awkward and estranging it is for a Jew, Muslim, Atheist, or anyone else not practicing the holiday under the same terms as a Christian. Especially when it comes in such high frequency.

I must admit however, that as soon as I left, my mild outrage transformed into radical jealousy. When these people leave and express their sentiments in the form of prayer they actually believe that they are doing practical good towards helping her get well. They leave 100% confident that their supernatural deity will listen to their pleading and intervene for her well-being. Meanwhile I leave deeply frightened and concerned for my friend and feeling utterly helpless. As of yesterday the doctors still aren’t sure of what she has and she’s on a regular supply of morphine to minimize her pain, and there’s nothing I can do about it.

I find myself desperately wishing I was capable of believing something I know to be false.

If you read my previous post, you already know that I was raised Christian and that I alone out of my God-fearing family have turned atheist.  My brother Mike I’m not too sure about.  He isn’t an active Christian but as far as I know he still believes in God. Anyways, although I haven’t told my parents outright that I no longer believe in God, I’m beginning to suspect that they are figuring it out.

They like to drop these not-so-subtle hints that I should be going back to church or that God is working in my life.  I generally just shrug these suggestions off to avoid a conflict but there was one instance when I could not resist a rebuttal.

One night I was up late with my Dad watching some Discovery or NOVA special on really crazy-awesome bugs.  One of the bugs covered was the bombardier beetle which is a remarkable insect that is renowned for its ability to defend itself by firing a mix of boiling toxic chemicals out of glands in different locations on its body.  During the beetle’s segment, my Dad said, “You know, there’s a really interesting debate going on right now saying that this bug disproves evolution because there’s no way that it could have evolved those chemicals separately by themselves because they serve no other purpose and because when they mix they explode.”  He said it offhandedly, probably not expecting a response.  I told him that although I didn’t know exactly how it happened, I was certain that evolution could have produced such an adaptation.

I happened to have my computer handy so I immediately started with Wikipedia to get a little background info on the beetle  and find out exactly how it evolved so I could explain it to Dad.  There wasn’t much in the Wiki article, so I followed the sources links at the bottom of the page to talkorgins.org.  There I found an entry that explained that the person who claimed that the two chemicals (hydroquinones and hydrogen peroxide) would explode when mixed was blatantly mistaken, yet continues to use the argument in debates.  It also outlined a highly plausible, step-by-step series of events that explain how the mechanism evolved.  I promptly sent him the link.  Unfortunately he didn’t get to read it until about a week later and he didn’t really say much about it.  I like to think he didn’t say much because he knew he had no counter-argument.

If you’re interested in reading that talkorgins entry you can find it here.