The path from science to alarmism: How science gets twisted before it gets to you



Source.


Today’s post is long. It’s long because it involves the winding path that science can take from ignition to exploding into the public view… and how the twists and turns in that path can result in a skewed representation and understanding of the science. Read the whole thing. It focuses on an example that involves autism–which seems to pop up in skewed representations every day–but certainly this path from science to you, the consumer, happens with scientific information in general. The author is Jess, who blogged this originally at “Don’t Mind the Mess” and graciously gave us permission to reproduce it here. Jess, an attorney with a B.S. in biochemistry, parent of an autistic child and brand new baby, and self-described “Twitter fiend,” tweets as @JessicaEsquire
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I am putting my foot down.
As the parent of an autistic child I hear a lot about vaccines and about half a million other things that people think cause autism.
I’m hyperaware of the attention autism gets in the media. So I know about the CDC’s new stats on autism rates. I know about the debate on whether the increase in autism is due to more awareness and diagnosis or more actual occurrences. (Personally, I find the former to be a serious factor, though who’s to say how much.) And I see all the articles that come out week after week about the millions of things that are linked to autism.
There’s a recurring problem here. Valuable research is done. Research is disseminated. Information is reported. Articles are read. Findings are spread. What starts in a lab ends up in a Facebook status. What starts as truth ends up as mistruth in something like a child’s game of telephone. Along the way, piece by piece, truth fades away in favor of headlines and pageviews and gossip.
It’s getting just plain stupid. I’m starting to suspect these articles have nothing to do with serious research but with a search for traffic and hype, an attempt to ride the wave of a trendy topic as concerned parents read every horror story they can find.
A particularly egregious one came up recently. This one doesn’t just cite some random correlation. This one is just plain making things up. The problems here just pile one on top of the other. So let’s consider it piece by piece, a case study in how real research becomes misinformation.

Part One: Research

It starts with scientists. It starts with research. They write up their findings and publish them in a peer-reviewed scientific journal. In this case there are several papers published over a few years about chemicals and their link to brain development. They cover a wide variety of issues and present a wide variety of conclusions. All of them suggest further study.
Maybe they have bad methodology or use statistics incorrectly. Only a few people would ever know the difference. That’s not my concern today. Bad science is one thing, but bad information on good science is another. So let’s assume we have good, solid science in this research.

Part Two: The Conference

Scientists and researchers with similar interests get together and discuss their findings. It’s not that difference from any other conference. There are panels and presentations.

Part Three: The Op-Ed

Next, a group that works on environmental hazards for children publishes a paper. Not a research study but an op-ed in a peer-reviewed journal. In this op-ed they review the conference from Part Two and encourage the study of environmental factors and their relationship to neurodevelopment disorders. Autism is one of many neuro-ish disorders and is mentioned by name in the piece and its title. It’s unclear to me why they zero in on autism. They have a couple vague pieces of evidence that are autism-specific, but the vast majority of what they’re looking at has never been demonstrated to have any kind of relationship to autism, not even a correlation.
Problem #1 is the unnecessary autism name-checking. Problem #2 is much worse, it’s the list of 10 chemicals they suggest for future study. The list itself isn’t a bad idea, I guess. They’re suggesting places for potential research, which certainly needs to be done. But it does reek a little bit of the kind of thing magazines do, you know what I mean, 10 Ways To Get Your Guy All Fired Up! and such. Still, it’s their prerogative.
So let’s examine their evidence for these suggestions. They cite at least one paper for each of these chemicals. I checked them all. The vast majority of them have never shown any connection to Autism (or even ADHD, another diagnosis they name-check). In fact, many of them show that with exposure to these chemicals, the outcome differentials between exposure and non-exposure is 5 IQ points.
FIVE IQ POINTS. Statistically significant? Perhaps. Practically important for a parent? No.
IQ itself is a strange and vague thing. And 5 points isn’t going to move your super-genius down to the level of an average person They’d still be a super-genius. And adding 5 points to someone with severe deficits isn’t going to make them average, either. It’s hard to imagine what difference you’d see between two people whose IQ’s are 5 points apart.
Such statistical differences may well be a sign to warrant further study. And they may be a sign that these chemicals affect neurological development. But it’s getting a bit ahead of ourselves to say they are suspected of being tied to autism. Many of these papers are in areas of research that are just beginning. Many of them involve homogeneous groups (for example, all the participants are Mexican-American migrant workers) which makes issues of genetics and heredity very difficult to account for. Many involve parents self-reporting by filling out surveys rather than having the children examined by professionals.
Let’s be fair. These are the very beginnings of research. You’ll need to do all sorts of rigorous testing and consideration to make real connections. Of course more research is needed. And it’s important that we keep that in mind as we move forward.
(Though, of course, no one else will.)

Part Four: The Press Release

The op-ed is about publicity so it’s the beginning of the problem. But it gets worse. A press release comes out with the list of ten chemicals and already the twisting starts. These are chemicals suggested for further research, but suddenly they’re a ”List of the Top Ten Toxic Chemicals Suspected to Cause Autism and Learning Disabilities.” This, unsurprisingly, is the headline you’ll see all over the internet when news organizations report on the press release. Already it’s turned from suggestions for research into a watchlist.
It gets worse. The press release has this second headline:
The editorial was published alongside four other papers — each suggesting a link between toxic chemicals and autism.
No, actually that’s not at all accurate.
Let’s start with the first paper, which examines the possibility of a connection between maternal smoking and autism. What’s their conclusion?
The primary analyses indicated a slightly inverse association with all ASDs[.]
What does that mean? Among the autistic kids vs. regular kids, there was actually LESS maternal smoking in the autism group. The paper does point out that when it comes to “subgroups,” for instance high-functioning ASD or Asperger’s, there may be a possibly positive relationship. But there are so many caveats I can’t even get to them all. Let’s just take this one:
The ASD subgroup variables were imperfect, relying on the child’s access to evaluation services and the documentation by a myriad of community providers, rather than direct clinical observation.
This means that when they’re saying some groups of ASD kids may have this relationship, they didn’t actually classify these kids. They never saw these kids. They’re relying on data collected by other people. Not even by a consistent set of people. It comes from 11 different states and who knows how many providers. Who’s to say how accurate any of it is. And who’s to say whether these kids are correctly classified at their particular place on the spectrum.
So take all that with a whole jar full of salt and you’re still looking at, overall, no connection with smoking. If anything, the data would indicate smoking has LESS autism rather than more.
After this there are 2 papers on the same chemical. One of them does not contain the word “autism” anywhere. (One of its references has it, but nowhere does it appear in the text of their paper.) The second paper is better. It focuses on the chemical’s effects in particular processes which have been linked to autism. This is very micro-scale science, there are no people involved, just cells and chemicals. It’s important research, but there’s a long stretch between cellular interactions and a person’s diagnosis. It didn’t involve any analysis with autistic individuals. This is certainly the most useful paper of the bunch by a long shot, but it still just sets the stage for further research.
The fourth paper is a review. That means it asserts no new information but summarizes the research on a particular issue, specifically pesticides and autism. Technically I suppose it does assert a link, but none of this is new information.
So I think we’ve pretty much destroyed the headline in that press release. There were not 4 articles suggesting a connection between chemicals and autism.
Is it likely that the writers who take this press release and write articles on it are going to read the papers it cites? Are they going to realize that what they’re saying isn’t actually true? They should. Of course they should. But they don’t.
This list has chemicals suspected of being tied to neurological development. And we should just leave it at that. It’s not that they shouldn’t be studied. They should. But we shouldn’t be throwing out buzzwords like ADHD and Autism when the research doesn’t show any firm data.

Part Five: News Articles

This is a process, though. First research, then op-ed, then press release and finally news articles. So what’s the headline of our news article? “Top 10 Chemicals Most Likely to Cause Autism and Learning Disabilities.” Guilty of serious fearmongering, no? A more accurate title may be: Researchers propose list of chemicals potentially tied to neurological development for further study. But I doubt anyone’s going to write that.
The article itself, to be fair, is full of caveats. The reasons for the increase in autism are “controversial.” There is a “gap in the science.”  But then you get a sentence like this:
But clearly, there is more to the story than simply genetics, as the increases are far too rapid to be of purely genetic origin.
Clearly? Clearly says who? What source says it’s too rapid? The author certainly isn’t a reliable source. She is Robyn O’Brien, a writer for Prevention who posted this article. Her scientific credentials are nonexistent. She is a former financial analyst who now writes about the food industry. She has an MBA, and her undergraduate was in French and Spanish.
Full disclosure: I have a B.S. in Biochemistry, but I feel I’m unqualified to write this article. I’d much rather it be written by someone with a PhD. I’m married to a PhD, which has given me a lot more exposure to science since leaving school, but I fully acknowledge that I shouldn’t be the one doing this. I know how to read a scientific article and examine its conclusions, but I certainly am not someone who can tell you if their methods and analysis are correct.
But I’m talking because there aren’t enough people talking about it. Because the PhD’s aren’t generally science writers. They are scientists. They write about their research in journals, not in the newspaper. And certainly not on a blog for a healthy living magazine.
The author goes on to restate the inaccurate subheadline of the press release verbatim.
In the end she suggests things like buying organic produce, opening your windows and buying BPA-free products.
This is part 5 of our process, but it’s where many of us start. Many of us will only read this article and not the press release or the op-ed or the research papers. Most of us aren’t qualified to do so, all we have is this article. Well, we have that and what other people tell us. Which leads us to our next step.

Part Six: Readers

The article is frustrating, but I can only get so mad. She is saying what the scientists told her to say. She has even included some cautionary language. The problem is that when writing for laymen, you have to be careful.
And with AUTISM? You have to be really careful. Just for you I’m going to venture into the comments to this article to show you how people have responded.
–How about we quit injecting our kids with aluminum, formaldehyde and the rest of the toxic stew that they call vaccines — we bypass every natural defense our bodies have (skin, saliva, stomach acid) to put these things directly in the blood stream.
–Thank you Robyn for always providing sound information to continue guiding our decisions.
–What about heavy metals like Arsenic that are trapped in soils that our “organic” brown rice is growing in to be made into brown rice syrup to sweeten organic foods and baby formula? Not to mention the reports coming in regarding the radiation and contamination from Fukushimi that has reached the west coast an is spreading across this country in the produce and even the pollen…
–Unvaccinated children are some of the healthiest little people on the planet. As far as the Autism link, who really knows but why risk it.
–Thank you for this information. It confirms to me that we should keep doing what we are doing. It also helps me to enforce our no shoes policy in our home. Some people are so disrespectful and just don’t take them off and I hate to sound like a nag and ask even though they already know its what we prefer.
Thankfully there are some people in there who take the writer to task, but how is a reader to trust any one commenter over another? You have no way of knowing from a comment what someone’s experiences or qualifications are.
There’s a reason we need responsible scientific reporting. I’m all for the open dissemination of information, but I’m also aware of what happens when people read something they don’t understand.
autism FB The Whole Truth About Autism
I encountered this FB conversation the other day. Usually I overlook such things but I could not help myself. I jumped in. I tried hard to be polite and present facts. When all that was over, no one was convinced. The response?
autism FB 2 The Whole Truth About Autism
Enough articles on vaccines and people are scared even without evidence. Enough headlines and people don’t bother reading articles. It doesn’t matter how much is retracted or debunked, the damage is done.
We need responsible science reporting. We need responsible reporting, period. I’ve seen plenty of lazy articles on Supreme Court opinions that lead me to read the opinion myself only to realize that they’ve stated the conclusions all wrong.
I don’t want to go on all day, but I do feel like it’s important for us to put our foot down and demand better.
We aren’t all scientists. But we can ask for science writers with the appropriate qualifications. We can ask for links and citations in their articles. (I spent quite some time tracking everything down for this post, and luckily I’m relatively familiar with looking up scientific articles online.) We can ask for articles that show failed connections. It doesn’t all have to be “Autism linked to X” there’s plenty of “Autism not linked to Y” that happens in these studies but you never see that, do you?
As for us laymen, we have to find our own trusted experts. Ask your pediatrician. And if your pediatrician’s not qualified (most of them are MD’s but not PhD’s) ask them if they have a trusted source. Track down specialists in Autism with PhD’s and ask them what they think of the research. Find reliable books and articles and spread them to your friends. We can’t necessarily do a lot, but we can do our part to stop the spread of misinformation and demand better.


These views are the opinion of the author and do not necessarily either reflect or disagree with those of the DXS editorial team.
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We also suggest

Science, health, medical news freaking you out? Do the Double X Double-Take first

Handy short-form version.

Have you seen the headlines? Skip them
You’ve probably seen a lot of headlines lately about autism and various behaviors, ways of being, or “toxins” that, the headlines tell you, are “linked” to it. Maybe you’re considering having a child and are mentally tallying up the various risk factors you have as a parent. Perhaps you have a child with autism and are now looking back, loaded with guilt that you ate high-fructose corn syrup or were overweight or too old or too near a freeway or not something enough that led to your child’s autism. Maybe you’re an autistic adult who’s getting a little tired of reading in these stories about how you don’t exist or how using these “risk factors” might help the world reduce the number of people who are like you.

Here’s the bottom line: No one knows precisely what causes the extremely diverse developmental difference we call autism. Research from around the world suggests a strong genetic component [PDF]. What headlines in the United States call an “epidemic” is, in all likelihood, largely attributable to expanded diagnostic inclusion, better identification, and, ironically, greater awareness of autism. In countries that have been able to assess overall population prevalence, such as the UK, rates seem to have held steady at about 1% for decades, which is about the current levels now identified among 8-year-olds in the United States. 

What anyone needs when it comes to headlines honking about a “link” to a specific condition is a mental checklist of what the article–and whatever research underlies it–is really saying. Previously, we brought you Real vs Fake Science: How to tell them apart. Now we bring you our Double X Double-Take checklist. Use it when you read any story about scientific research and human health, medicine, biology, or genetics.

The Double X Double-Take: What to do when reading science in the news
1. Skip the headline. Headlines are often misleading, at best, and can be wildly inaccurate. Forget about the headline. Pretend you never even saw the headline.

2. What is the basis of the article? Science news originates from several places. Often it’s a scientific paper. These papers come in several varieties. The ones that report a real study–lots of people or mice or flies, lots of data, lots of analysis, a hypothesis tested, statistics done–is considered “original research.” Those papers are the only ones that are genuinely original scientific studies. Words to watch for–terms that suggest no original research at all–are “review,” “editorial,” “perspective,” “commentary,” “case study” (these typically involve one or only a handful of cases, so no statistical analysis), and “meta-analysis.” None of these represents original findings from a scientific study. All but the last two are opinion. Also watch for “scientific meeting” and “conference.” That means that this information was presented without peer review at a scientific meeting. It hasn’t been vetted in any way.

3. Look at the words in the article. If what you’re reading contains words like “link,” “association,” “correlation,” or “risk,” then what the article is describing is a mathematical association between one thing (e.g., autism) and another (e.g., eating ice cream). It is likely not describing a biological connection between the two. In fact, popular articles seem to very rarely even cover scientific research that homes in on the biological connections. Why? Because these findings usually come in little bits and pieces that over time–often quite a bit of time–build into a larger picture showing a biological pathway by which Variable 1 leads to Outcome A. That’s not generally a process that’s particularly newsworthy, and the pathways can be both too specific and extremely confusing.

4. Look at the original source of the information. Google is your friend. Is the original source a scientific journal? At the very least, especially for original research, the abstract will be freely available. A news story based on a journal paper should provide a link to that abstract, but many, many news outlets do not do this–a huge disservice to the interested, engaged reader. At any rate, the article probably includes the name of a paper author and the journal of publication, and a quick Google search on both terms along with the subject (e.g., autism) will often find you the paper. If all you find is a news release about the paper–at outlets like ScienceDaily or PhysOrg–you are reading marketing materials. Period. And if there is no mention of publication in a journal, be very, very cautious in your interpretation of what’s being reported.

5. Remember that every single person involved in what you’re reading has a dog in the hunt. The news outlet wants clicks. For that reason, the reporter needs clicks. The researchers probably want attention to their research. The institutions where the researchers do their research want attention, prestige, and money. A Website may be trying to scare you into buying what they’re selling. Some people are not above using “sexy” science topics to achieve all of the above. Caveat lector

6. Ask a scientist. Twitter abounds with scientists and sciencey types who may be able to evaluate an article for you. I receive daily requests via email, Facebook, and Twitter for exactly that assistance, and I’m glad to provide it. Seriously, ask a scientist. You’ll find it hard to get us to shut up. We do science because we really, really like it. It sure ain’t for the money. [Edited to add: But see also an important caveat and an important suggestion from Maggie Koerth-Baker over at Boing Boing and, as David Bradley has noted over at ScienceBase, always remember #5 on this list when applying #6.] 

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Case Study
Lately, everyone seems to be using “autism” as a way to draw eyeballs to their work. Below, I’m giving my own case study of exactly that phenomenon as an example of how to apply this checklist.

1. Headline: “Ten chemicals most likely to cause autism and learning disabilities” and “Could autism be caused by one of these 10 chemicals?” Double X Double-Take 1: Skip the headline. Check. Especially advisable as there is not one iota of information about “cause” involved here.

2. What is the basis of the articleEditorialConference. In other words, those 10 chemicals aren’t something researchers identified in careful studies as having a link to autism but instead are a list of suspects the editorial writers derived, a list that they’d developed two years ago at the mentioned conference. 

3. Look at the words in the articles. Suspected. Suggesting a link. In other words, what you’re reading below those headlines does not involve studies linking anything to autism. Instead, it’s based on an editorial listing 10 compounds [PDF] that the editorial authors suspect might have something to do with autism (NB: Both linked stories completely gloss over the fact that most experts attribute the rise in autism diagnoses to changing and expanded diagnostic criteria, a shift in diagnosis from other categories to autism, and greater recognition and awareness–i.e., not to genetic changes or environmental factors. The editorial does the same). The authors do not provide citations for studies that link each chemical cited to autism itself, and the editorial itself is not focused on autism, per se, but on “neurodevelopmental” derailments in general.

4. Look at the original source of information. The source of the articles is an editorial, as noted. But one of these articles also provides a link to an actual research paper. The paper doesn’t even address any of the “top 10″ chemicals listed but instead is about cigarette smoking. News stories about this study describe it as linking smoking during pregnancy and autism. Yet the study abstract states that they did not identify a link, saying “We found a null association between maternal smoking and pregnancy in ASDs and the possibility of an association with a higher-functioning ASD subgroup was suggested.” In other words: No link between smoking and autism. But the headlines and how the articles are written would lead you to believe otherwise. 

5. Remember that every single person involved has a dog in this hunt. Read with a critical eye. Ask yourself, what are people saying vs what real support exists for their assertions? Who stands to gain and in what way from having this information publicized? Think about the current culture–does the article or the research drag in “hot” topics (autism, obesity, fats, high-fructose corn syrup, “toxins,” Kim Kardashian) without any real basis for doing so? 

6. Ask a scientist. Why, yes, I am a scientist, so I’ll respond. My field of research for 10 years happens to have been endocrine-disrupting compounds. I’ve seen literally one drop of a compound dissolved in a trillion drops of solvent shift development of a turtle from male to female. I’ve seen the negative embryonic effects of pesticides and an over-the-counter antihistamine on penile development in mice. I know well the literature that runs to the thousands of pages indicating that we’ve got a lot of chemicals around us and in us that can have profound influences during sensitive periods of development, depending on timing, dose, species, and what other compounds may be involved. Endocrine disruptors or “toxins” are a complex group with complex interactions and effects and can’t be treated as a monolith any more than autism should be.

What I also know is that synthetic endocrine-disruptors have been around for more than a century and that natural ones for far, far longer. Do I think that the “top 10″ chemicals require closer investigation and regulation? Yes. But not because I think they’re causative in some autism “epidemic.” We’ve got sufficiently compelling evidence of their harm already without trying to use “autism” as a marketing tool to draw attention to them. Just as a couple of examples: If coal-burning pollution (i.e., mercury) were causative in autism, I’d expect some evidence of high rates in, say, Victorian London, where the average household burned 11 tons of coal a year. If modern lead exposures were causative, I’d be expecting records from notoriously lead-burdened ancient Rome containing descriptions of the autism epidemic that surely took it over. 

Bottom line: We’ve got plenty of reasons for concern about the developmental effects of the compounds on this list. But we’ve got very limited reasons to make autism a focal point for testing them. Using the Double X Double-Take checklist helps demonstrate that.

By Emily Willingham, DXS managing editor 

Good Deeds, Good Science: Autism Research Foundation

Happy Leap Day!

How often have you wished for an extra hour or extra day to get everything you need done? At the Autism Science Foundation (ASF), we want to make the most of this special leap day by using it to help autism science leap forward.

Thanks to your support, for the last two years we have provided funding for autism stakeholders (parents, individuals with autism, teachers, students, etc) to attend the International Meeting for Autism Research (IMFAR). All donations made today, February 29, 2012, will go directly to our IMFAR Travel Grants program, helping us provide more scholarships to IMFAR 2012 in Toronto where they will share their real world autism experience with scientists. These stakeholders will then bring the latest autism science back into our communities helping the science take a giant leap forward.

After attending IMFAR, past grant recipients have:
- Organized a five day autism science seminar at Barnard College
- Presented critical autism research information to nurses in Philadelphia
- Produced multiple blog posts that reached thousands of readers around the world
- Organized an autism awareness club and speaker series at Yale College

And thanks to a generous donor, all donations made today (February 29, 2012) will be matched dollar for dollar for an extra big leap. 

Do something special with this extra day of 2012 and help leap science forward. Please make a donation today!

BTW - It’s no coincidence that applications for our IMFAR travel grants are due today. Thinking of applying? Click here to learn more.

The Autism Science Foundation was founded in 2009 as a nonprofit corporation organized for charitable and educational purposes, and exempt from taxation under section 501(c)(3) of the IRS code.
The Autism Science Foundation’s mission is to support autism research by providing funding and other assistance to scientists and organizations conducting, facilitating, publicizing and disseminating autism research. The organization also provides information about autism to the general public and serves to increase awareness of autism spectrum disorders and the needs of individuals and families affected by autism.

Crowdfunding on the Brain: Finding Biomarkers for Early Autism Diagnosis

By Biology Editor, Jeanne Garbarino


If a child is diagnosed with autism spectrum disorder (ASD), it is because they have gone through a number of rigorous behavioral tests, often over a period of time, and never straightforward. Of course, this time can be a stressful for parents or caregivers, and sometimes the answers can lead to even more questions. One solution to the waiting and uncertainty would be to have a medical test that could more easily diagnose ASD. However, no one has been able to identify biomarkers – molecules in the body that can help define a specific medical condition – for the condition. Without this type of information, it is not possible to create a diagnostic test for autism.


Having been through this process with their son, who is on the autism spectrum, Clarkson University scientists Costel Darie and Alisa Woods have decided to work together to help address this issue. An interdisciplinary laboratory that combines hardcore proteomics (the study of the proteins we make) with cognitive neuroscience is probably not what you think of when it comes to running a family business. But for Darie and Woods, “marriage” has many meanings. This husband and wife team has combined their brainpower to embark on a scientific journey toward understanding some of the biochemistry behind autism, and they are walking on an increasingly popular path to help finance their work: crowdfunding.


A major goal of the Darie Lab is to identify biomarkers that are associated with autism and then to create a medical test to help alleviate some of the frustrations that come with the ASD diagnostic process. Using a technology called high-definition mass spectrometry, the Darie Lab has outlined a project to figure out the types of proteins that are in the saliva or blood of children with ASD and compare these protein profiles to the saliva or blood from children who are not on the autism spectrum. If the Darie Lab is successful, they might be able to help create a diagnostic test for early autism detection, which would undoubtedly fill a giant void in the field of autism research and treatment.


Here is how the experiment will work: The members of the Darie Lab will collect saliva (and/or blood) samples from children, half of whom are on the autism spectrum and half of whom are not. The researchers will prepare the saliva or blood and collect the proteins. Each protein will be analyzed by a high definition mass spectrometer, which is basically a small scale for measuring the weight and charge of a protein. The high definition mass spectrometer will transfer information about the proteins to a computer, with special software allowing the Darie Lab investigators to figure out the exact makeup of proteins in each sample.


The bottleneck when it comes to these experiments is not getting samples (saliva and blood are easy to collect), and it isn’t the high-tech high-definition mass spectrometer because they have access to one.  Rather, the bottleneck comes from the very high cost of the analytical software they need. Because this software was not included in their annual laboratory budget but is critical to conducting this experiment, the Darie Lab is raising money through crowdfunding.


Why I think a contribution is worth the investment: Technology is always advancing, especially when it comes to protein biochemistry. The high-definition mass spectrometer is a recent technology, and according to the Darie Lab, they have been able to identify over 700 proteins in the saliva alone. This is quite an incredible step up from traditional mass spectrometers, which could detect only around 100 proteins in saliva. Just because we haven’t been able to identify biomarkers for autism in the past doesn’t mean we can’t do it now. 

In addition to the use of this new technology, the Darie Lab presents some compelling preliminary evidence for a difference in protein profiles between those with ASD and those who do not have ASD. While they’ve examined only three autistic people and compared them to three non-ASD individuals, the two groups were clearly distinct in their saliva protein profiles. If this pattern holds up with an increased number of study participants, the implications could be quite significant for autism research.      
Preliminary data from the Darie Lab shows that there are saliva proteins showing a 20X or greater
difference  between ASD (ovals) versus sibling non-ASD controls (rectangles).

If you decide to kick in some funds, your good deed will not go unrewarded. As a thank-you for contributing, the Darie Lab has offered up a few cool perks, including high-quality prints of microscopic images in the brain. 



If you are looking for a good cause, look no further. I am excited to see how the Darie Lab crowdfund experience goes, and I wish them all the best in their quest, both as professionals and as parents.  To find out more, or to make a donation, visit the Darie Lab RocketHub page.

Fluorescent images of the brain, available to those donating $100 or more.
The opinions expressed in this post do not necessarily agree or conflict with those of the DXS editorial team and contributors.

Mental illness, autism, and mass murder, and why Joe Scarborough needs to stop talking

Via Wikimedia Commons. Public domain. 

[Ed. note: Some of this information comes from a post that previously appeared at The Biology Files following the shooting massacre in Arizona targeting U.S. Rep. Gabrielle Giffords, among others.]

By Emily Willingham 

Today, Joe Scarborough at MSNBC warned viewers not to generalize about the horrific events in Aurora, CO, and then proceeded to opine that the killer in question was “on the autism scale.” I’m not exactly sure what “on the autism scale” means, as I’ve never in all my years of involvement in the autism community come across such a device, but many of us in that community were waiting–nay, expecting–something like this almost from the minute we learned who had committed these murders. Too bad it came from a parent member of that community.

Hey, Joe, you’ve got a gun in your hand, and it’s not like the one that the who-knows-what-his-disorder-is murderer in Aurora used. No. Your weapon is of a more subtle nature, and you wield it from a venue that reaches millions of people who don’t know that the ammo you’re firing is empty bullshit. But that bullshit ends up smearing the autistic community as violent criminals capable of all manner of psychotic behavior, including the taking of innocent lives and the well-planned rigging of an apartment building with dangerous explosives. And you must understand this on some level, as you have a son who is on the autism spectrum.

Here’s the thing, Joe. You’re conflating what can be very personal, nonfatal aggression of an overwhelmed autistic person with the wanton and willful and carefully planned destruction of total strangers in a crowded theater. Yes, some autistic people are aggressive, in the moment, in response to a moment, to being overwhelmed and not understood, to being mishandled and misused. That sort of aggression is a very, very different animal from the sort of cold, calculated malevolence that leads a young man to inflict tragedy across a large swath of humanity, total strangers to him, arriving with a measured burst of deadly force before calmly surrendering himself to authorities. You, Joe Scarborough, see that behavior as somehow “on the autism scale.” Anyone who has even a mild grasp of autism knows how very far from reality that kind of behavior is for an autistic person. 

So let’s talk about violence. 
A look at the violence literature reveals two rough categories of violent brain and genetics: the brain of the impulsively or hostilely violent and the brain of the proactive, or instrumentally violent–the one who carefully plans the violent act, rather than committing it in the heat of the moment. Impulsive violence, thanks to its unpredictability and relative ubiquity, seems to get the bulk of the attention. Proactive violence, which encompasses the planned violence of war, is a different animal altogether. And psychopathic instrumental violence may well be the most terrifying of them all. The two appear to have very different underlying mechanisms and origins, as well:

Biological models of violence have identified distinct neural patterns that characterize each type of violence. For example, the “low-arousal” aggressor more likely to commit instrumental violence is underreactive and responds sluggishly to stressors. In contrast, the “high-arousal” aggressor who is more prone to hostile violence tends to be hypervigiliant and easily frustrated 
In humans, instrumental aggression is roughly analogous to predatory aggression although it is limited to intraspecies behavior….Similarly, emotional or hostile aggression in humans could be considered the analogue of defensive aggression in response to a threat or perceived threat.

No one–and I mean, no one–has a clue what drove this man to commit his heinous crimes. What we do know is that he planned his hellish introduction into our psyches for months beforehand, carefully accumulating all the accouterments needed to generate a national and personal nightmare. What we also know is that he carefully planned his violent act; it was not, like an autistic meltdown, an act of the moment, an unplanned reaction

And you’re wrong on some other counts as well, demonstrating the real dangers of a weapon like yours in the hands of the uninformed. You said that the minute you heard about the shooting, you knew it would be young white male, probably from “an affluent neighborhood.” While being young, white, and male may fit the profile of many serial killers, mass murders are a different breed. They come from different backgrounds and ethnicities, but most share a single motivation: revenge. When they go beyond personal connections in their targets and kill total strangers, that revenge is usually against a society the killer thinks has wronged him. 

Other features in common are being male, being a “loner,” and feeling alienated from the world. For the record, “autistic” does not equate with “loner” or “male,” as much as you or the news media would like to distort it into that mold. Research, such as it is, suggests that the more a killer goes impersonal and targets strangers, the more likely a mental illness is to be involved. While that mental illness is usually paranoid schizophrenia, we must all remember that there are many, many more murderers in this world who are not schizophrenic than there are schizophrenics who commit this kind of violence. The coupling is not inevitable or even common. Indeed, better predictors of violence are unemployment, physical abuse, and recent divorce. The killer in the Aurora case had recently in effect become unemployed, having left graduate school and done poorly on spring exams. 

I’ll close with this final observation: Autism is a disorder that is present from birth or very soon after. There are, however, other mental disorders and mental breaks that occur, particularly in young men and particularly at vulnerable developmental periods like adolescence and early adulthood. Not only does autism not fit here simply by virtue of its lifelong presence, but also, it’s not something that just kinda shows up when a man turns 24 years old. 

The man who destroyed so many lives showed several signs of extreme stress prior to his murderous rampage. Were these stressors the trigger for him? That I cannot say. But I can say that stress does not bring on autism in one’s 20s, and autism at any age doesn’t lead to carefully calculated revenge killings of innocent strangers. So, Joe, why don’t you just put down your weapon and back away… as quickly as you can.

These views are the opinion of the author and do not necessarily either reflect or disagree with those of the DXS editorial team. 

Biology Explainer: The big 4 building blocks of life–carbohydrates, fats, proteins, and nucleic acids

The short version
  • The four basic categories of molecules for building life are carbohydrates, lipids, proteins, and nucleic acids.
  • Carbohydrates serve many purposes, from energy to structure to chemical communication, as monomers or polymers.
  • Lipids, which are hydrophobic, also have different purposes, including energy storage, structure, and signaling.
  • Proteins, made of amino acids in up to four structural levels, are involved in just about every process of life.                                                                                                      
  • The nucleic acids DNA and RNA consist of four nucleotide building blocks, and each has different purposes.
The longer version
Life is so diverse and unwieldy, it may surprise you to learn that we can break it down into four basic categories of molecules. Possibly even more implausible is the fact that two of these categories of large molecules themselves break down into a surprisingly small number of building blocks. The proteins that make up all of the living things on this planet and ensure their appropriate structure and smooth function consist of only 20 different kinds of building blocks. Nucleic acids, specifically DNA, are even more basic: only four different kinds of molecules provide the materials to build the countless different genetic codes that translate into all the different walking, swimming, crawling, oozing, and/or photosynthesizing organisms that populate the third rock from the Sun.

                                                  

Big Molecules with Small Building Blocks

The functional groups, assembled into building blocks on backbones of carbon atoms, can be bonded together to yield large molecules that we classify into four basic categories. These molecules, in many different permutations, are the basis for the diversity that we see among living things. They can consist of thousands of atoms, but only a handful of different kinds of atoms form them. It’s like building apartment buildings using a small selection of different materials: bricks, mortar, iron, glass, and wood. Arranged in different ways, these few materials can yield a huge variety of structures.

We encountered functional groups and the SPHONC in Chapter 3. These components form the four categories of molecules of life. These Big Four biological molecules are carbohydrates, lipids, proteins, and nucleic acids. They can have many roles, from giving an organism structure to being involved in one of the millions of processes of living. Let’s meet each category individually and discover the basic roles of each in the structure and function of life.
Carbohydrates

You have met carbohydrates before, whether you know it or not. We refer to them casually as “sugars,” molecules made of carbon, hydrogen, and oxygen. A sugar molecule has a carbon backbone, usually five or six carbons in the ones we’ll discuss here, but it can be as few as three. Sugar molecules can link together in pairs or in chains or branching “trees,” either for structure or energy storage.

When you look on a nutrition label, you’ll see reference to “sugars.” That term includes carbohydrates that provide energy, which we get from breaking the chemical bonds in a sugar called glucose. The “sugars” on a nutrition label also include those that give structure to a plant, which we call fiber. Both are important nutrients for people.

Sugars serve many purposes. They give crunch to the cell walls of a plant or the exoskeleton of a beetle and chemical energy to the marathon runner. When attached to other molecules, like proteins or fats, they aid in communication between cells. But before we get any further into their uses, let’s talk structure.

The sugars we encounter most in basic biology have their five or six carbons linked together in a ring. There’s no need to dive deep into organic chemistry, but there are a couple of essential things to know to interpret the standard representations of these molecules.

Check out the sugars depicted in the figure. The top-left molecule, glucose, has six carbons, which have been numbered. The sugar to its right is the same glucose, with all but one “C” removed. The other five carbons are still there but are inferred using the conventions of organic chemistry: Anywhere there is a corner, there’s a carbon unless otherwise indicated. It might be a good exercise for you to add in a “C” over each corner so that you gain a good understanding of this convention. You should end up adding in five carbon symbols; the sixth is already given because that is conventionally included when it occurs outside of the ring.

On the left is a glucose with all of its carbons indicated. They’re also numbered, which is important to understand now for information that comes later. On the right is the same molecule, glucose, without the carbons indicated (except for the sixth one). Wherever there is a corner, there is a carbon, unless otherwise indicated (as with the oxygen). On the bottom left is ribose, the sugar found in RNA. The sugar on the bottom right is deoxyribose. Note that at carbon 2 (*), the ribose and deoxyribose differ by a single oxygen.

The lower left sugar in the figure is a ribose. In this depiction, the carbons, except the one outside of the ring, have not been drawn in, and they are not numbered. This is the standard way sugars are presented in texts. Can you tell how many carbons there are in this sugar? Count the corners and don’t forget the one that’s already indicated!

If you said “five,” you are right. Ribose is a pentose (pent = five) and happens to be the sugar present in ribonucleic acid, or RNA. Think to yourself what the sugar might be in deoxyribonucleic acid, or DNA. If you thought, deoxyribose, you’d be right.

The fourth sugar given in the figure is a deoxyribose. In organic chemistry, it’s not enough to know that corners indicate carbons. Each carbon also has a specific number, which becomes important in discussions of nucleic acids. Luckily, we get to keep our carbon counting pretty simple in basic biology. To count carbons, you start with the carbon to the right of the non-carbon corner of the molecule. The deoxyribose or ribose always looks to me like a little cupcake with a cherry on top. The “cherry” is an oxygen. To the right of that oxygen, we start counting carbons, so that corner to the right of the “cherry” is the first carbon. Now, keep counting. Here’s a little test: What is hanging down from carbon 2 of the deoxyribose?

If you said a hydrogen (H), you are right! Now, compare the deoxyribose to the ribose. Do you see the difference in what hangs off of the carbon 2 of each sugar? You’ll see that the carbon 2 of ribose has an –OH, rather than an H. The reason the deoxyribose is called that is because the O on the second carbon of the ribose has been removed, leaving a “deoxyed” ribose. This tiny distinction between the sugars used in DNA and RNA is significant enough in biology that we use it to distinguish the two nucleic acids.

In fact, these subtle differences in sugars mean big differences for many biological molecules. Below, you’ll find a couple of ways that apparently small changes in a sugar molecule can mean big changes in what it does. These little changes make the difference between a delicious sugar cookie and the crunchy exoskeleton of a dung beetle.

Sugar and Fuel

A marathon runner keeps fuel on hand in the form of “carbs,” or sugars. These fuels provide the marathoner’s straining body with the energy it needs to keep the muscles pumping. When we take in sugar like this, it often comes in the form of glucose molecules attached together in a polymer called starch. We are especially equipped to start breaking off individual glucose molecules the minute we start chewing on a starch.

Double X Extra: A monomer is a building block (mono = one) and a polymer is a chain of monomers. With a few dozen monomers or building blocks, we get millions of different polymers. That may sound nutty until you think of the infinity of values that can be built using only the numbers 0 through 9 as building blocks or the intricate programming that is done using only a binary code of zeros and ones in different combinations.

Our bodies then can rapidly take the single molecules, or monomers, into cells and crack open the chemical bonds to transform the energy for use. The bonds of a sugar are packed with chemical energy that we capture to build a different kind of energy-containing molecule that our muscles access easily. Most species rely on this process of capturing energy from sugars and transforming it for specific purposes.

Polysaccharides: Fuel and Form

Plants use the Sun’s energy to make their own glucose, and starch is actually a plant’s way of storing up that sugar. Potatoes, for example, are quite good at packing away tons of glucose molecules and are known to dieticians as a “starchy” vegetable. The glucose molecules in starch are packed fairly closely together. A string of sugar molecules bonded together through dehydration synthesis, as they are in starch, is a polymer called a polysaccharide (poly = many; saccharide = sugar). When the monomers of the polysaccharide are released, as when our bodies break them up, the reaction that releases them is called hydrolysis.

Double X Extra: The specific reaction that hooks one monomer to another in a covalent bond is called dehydration synthesis because in making the bond–synthesizing the larger molecule–a molecule of water is removed (dehydration). The reverse is hydrolysis (hydro = water; lysis = breaking), which breaks the covalent bond by the addition of a molecule of water.

Although plants make their own glucose and animals acquire it by eating the plants, animals can also package away the glucose they eat for later use. Animals, including humans, store glucose in a polysaccharide called glycogen, which is more branched than starch. In us, we build this energy reserve primarily in the liver and access it when our glucose levels drop.

Whether starch or glycogen, the glucose molecules that are stored are bonded together so that all of the molecules are oriented the same way. If you view the sixth carbon of the glucose to be a “carbon flag,” you’ll see in the figure that all of the glucose molecules in starch are oriented with their carbon flags on the upper left.

The orientation of monomers of glucose in polysaccharides can make a big difference in the use of the polymer. The glucoses in the molecule on the top are all oriented “up” and form starch. The glucoses in the molecule on the bottom alternate orientation to form cellulose, which is quite different in its function from starch.

Storing up sugars for fuel and using them as fuel isn’t the end of the uses of sugar. In fact, sugars serve as structural molecules in a huge variety of organisms, including fungi, bacteria, plants, and insects.

The primary structural role of a sugar is as a component of the cell wall, giving the organism support against gravity. In plants, the familiar old glucose molecule serves as one building block of the plant cell wall, but with a catch: The molecules are oriented in an alternating up-down fashion. The resulting structural sugar is called cellulose.

That simple difference in orientation means the difference between a polysaccharide as fuel for us and a polysaccharide as structure. Insects take it step further with the polysaccharide that makes up their exoskeleton, or outer shell. Once again, the building block is glucose, arranged as it is in cellulose, in an alternating conformation. But in insects, each glucose has a little extra added on, a chemical group called an N-acetyl group. This addition of a single functional group alters the use of cellulose and turns it into a structural molecule that gives bugs that special crunchy sound when you accidentally…ahem…step on them.

These variations on the simple theme of a basic carbon-ring-as-building-block occur again and again in biological systems. In addition to serving roles in structure and as fuel, sugars also play a role in function. The attachment of subtly different sugar molecules to a protein or a lipid is one way cells communicate chemically with one another in refined, regulated interactions. It’s as though the cells talk with each other using a specialized, sugar-based vocabulary. Typically, cells display these sugary messages to the outside world, making them available to other cells that can recognize the molecular language.

Lipids: The Fatty Trifecta

Starch makes for good, accessible fuel, something that we immediately attack chemically and break up for quick energy. But fats are energy that we are supposed to bank away for a good long time and break out in times of deprivation. Like sugars, fats serve several purposes, including as a dense source of energy and as a universal structural component of cell membranes everywhere.

Fats: the Good, the Bad, the Neutral

Turn again to a nutrition label, and you’ll see a few references to fats, also known as lipids. (Fats are slightly less confusing that sugars in that they have only two names.) The label may break down fats into categories, including trans fats, saturated fats, unsaturated fats, and cholesterol. You may have learned that trans fats are “bad” and that there is good cholesterol and bad cholesterol, but what does it all mean?

Let’s start with what we mean when we say saturated fat. The question is, saturated with what? There is a specific kind of dietary fat call the triglyceride. As its name implies, it has a structural motif in which something is repeated three times. That something is a chain of carbons and hydrogens, hanging off in triplicate from a head made of glycerol, as the figure shows.  Those three carbon-hydrogen chains, or fatty acids, are the “tri” in a triglyceride. Chains like this can be many carbons long.

Double X Extra: We call a fatty acid a fatty acid because it’s got a carboxylic acid attached to a fatty tail. A triglyceride consists of three of these fatty acids attached to a molecule called glycerol. Our dietary fat primarily consists of these triglycerides.

Triglycerides come in several forms. You may recall that carbon can form several different kinds of bonds, including single bonds, as with hydrogen, and double bonds, as with itself. A chain of carbon and hydrogens can have every single available carbon bond taken by a hydrogen in single covalent bond. This scenario of hydrogen saturation yields a saturated fat. The fat is saturated to its fullest with every covalent bond taken by hydrogens single bonded to the carbons.

Saturated fats have predictable characteristics. They lie flat easily and stick to each other, meaning that at room temperature, they form a dense solid. You will realize this if you find a little bit of fat on you to pinch. Does it feel pretty solid? That’s because animal fat is saturated fat. The fat on a steak is also solid at room temperature, and in fact, it takes a pretty high heat to loosen it up enough to become liquid. Animals are not the only organisms that produce saturated fat–avocados and coconuts also are known for their saturated fat content.

The top graphic above depicts a triglyceride with the glycerol, acid, and three hydrocarbon tails. The tails of this saturated fat, with every possible hydrogen space occupied, lie comparatively flat on one another, and this kind of fat is solid at room temperature. The fat on the bottom, however, is unsaturated, with bends or kinks wherever two carbons have double bonded, booting a couple of hydrogens and making this fat unsaturated, or lacking some hydrogens. Because of the space between the bumps, this fat is probably not solid at room temperature, but liquid.

You can probably now guess what an unsaturated fat is–one that has one or more hydrogens missing. Instead of single bonding with hydrogens at every available space, two or more carbons in an unsaturated fat chain will form a double bond with carbon, leaving no space for a hydrogen. Because some carbons in the chain share two pairs of electrons, they physically draw closer to one another than they do in a single bond. This tighter bonding result in a “kink” in the fatty acid chain.

In a fat with these kinks, the three fatty acids don’t lie as densely packed with each other as they do in a saturated fat. The kinks leave spaces between them. Thus, unsaturated fats are less dense than saturated fats and often will be liquid at room temperature. A good example of a liquid unsaturated fat at room temperature is canola oil.

A few decades ago, food scientists discovered that unsaturated fats could be resaturated or hydrogenated to behave more like saturated fats and have a longer shelf life. The process of hydrogenation–adding in hydrogens–yields trans fat. This kind of processed fat is now frowned upon and is being removed from many foods because of its associations with adverse health effects. If you check a food label and it lists among the ingredients “partially hydrogenated” oils, that can mean that the food contains trans fat.

Double X Extra: A triglyceride can have up to three different fatty acids attached to it. Canola oil, for example, consists primarily of oleic acid, linoleic acid, and linolenic acid, all of which are unsaturated fatty acids with 18 carbons in their chains.

Why do we take in fat anyway? Fat is a necessary nutrient for everything from our nervous systems to our circulatory health. It also, under appropriate conditions, is an excellent way to store up densely packaged energy for the times when stores are running low. We really can’t live very well without it.

Phospholipids: An Abundant Fat

You may have heard that oil and water don’t mix, and indeed, it is something you can observe for yourself. Drop a pat of butter–pure saturated fat–into a bowl of water and watch it just sit there. Even if you try mixing it with a spoon, it will just sit there. Now, drop a spoon of salt into the water and stir it a bit. The salt seems to vanish. You’ve just illustrated the difference between a water-fearing (hydrophobic) and a water-loving (hydrophilic) substance.

Generally speaking, compounds that have an unequal sharing of electrons (like ions or anything with a covalent bond between oxygen and hydrogen or nitrogen and hydrogen) will be hydrophilic. The reason is that a charge or an unequal electron sharing gives the molecule polarity that allows it to interact with water through hydrogen bonds. A fat, however, consists largely of hydrogen and carbon in those long chains. Carbon and hydrogen have roughly equivalent electronegativities, and their electron-sharing relationship is relatively nonpolar. Fat, lacking in polarity, doesn’t interact with water. As the butter demonstrated, it just sits there.

There is one exception to that little maxim about fat and water, and that exception is the phospholipid. This lipid has a special structure that makes it just right for the job it does: forming the membranes of cells. A phospholipid consists of a polar phosphate head–P and O don’t share equally–and a couple of nonpolar hydrocarbon tails, as the figure shows. If you look at the figure, you’ll see that one of the two tails has a little kick in it, thanks to a double bond between the two carbons there.

Phospholipids form a double layer and are the major structural components of cell membranes. Their bend, or kick, in one of the hydrocarbon tails helps ensure fluidity of the cell membrane. The molecules are bipolar, with hydrophilic heads for interacting with the internal and external watery environments of the cell and hydrophobic tails that help cell membranes behave as general security guards.

The kick and the bipolar (hydrophobic and hydrophilic) nature of the phospholipid make it the perfect molecule for building a cell membrane. A cell needs a watery outside to survive. It also needs a watery inside to survive. Thus, it must face the inside and outside worlds with something that interacts well with water. But it also must protect itself against unwanted intruders, providing a barrier that keeps unwanted things out and keeps necessary molecules in.

Phospholipids achieve it all. They assemble into a double layer around a cell but orient to allow interaction with the watery external and internal environments. On the layer facing the inside of the cell, the phospholipids orient their polar, hydrophilic heads to the watery inner environment and their tails away from it. On the layer to the outside of the cell, they do the same.
As the figure shows, the result is a double layer of phospholipids with each layer facing a polar, hydrophilic head to the watery environments. The tails of each layer face one another. They form a hydrophobic, fatty moat around a cell that serves as a general gatekeeper, much in the way that your skin does for you. Charged particles cannot simply slip across this fatty moat because they can’t interact with it. And to keep the fat fluid, one tail of each phospholipid has that little kick, giving the cell membrane a fluid, liquidy flow and keeping it from being solid and unforgiving at temperatures in which cells thrive.

Steroids: Here to Pump You Up?

Our final molecule in the lipid fatty trifecta is cholesterol. As you may have heard, there are a few different kinds of cholesterol, some of which we consider to be “good” and some of which is “bad.” The good cholesterol, high-density lipoprotein, or HDL, in part helps us out because it removes the bad cholesterol, low-density lipoprotein or LDL, from our blood. The presence of LDL is associated with inflammation of the lining of the blood vessels, which can lead to a variety of health problems.

But cholesterol has some other reasons for existing. One of its roles is in the maintenance of cell membrane fluidity. Cholesterol is inserted throughout the lipid bilayer and serves as a block to the fatty tails that might otherwise stick together and become a bit too solid.

Cholesterol’s other starring role as a lipid is as the starting molecule for a class of hormones we called steroids or steroid hormones. With a few snips here and additions there, cholesterol can be changed into the steroid hormones progesterone, testosterone, or estrogen. These molecules look quite similar, but they play very different roles in organisms. Testosterone, for example, generally masculinizes vertebrates (animals with backbones), while progesterone and estrogen play a role in regulating the ovulatory cycle.

Double X Extra: A hormone is a blood-borne signaling molecule. It can be lipid based, like testosterone, or short protein, like insulin.

Proteins

As you progress through learning biology, one thing will become more and more clear: Most cells function primarily as protein factories. It may surprise you to learn that proteins, which we often talk about in terms of food intake, are the fundamental molecule of many of life’s processes. Enzymes, for example, form a single broad category of proteins, but there are millions of them, each one governing a small step in the molecular pathways that are required for living.

Levels of Structure

Amino acids are the building blocks of proteins. A few amino acids strung together is called a peptide, while many many peptides linked together form a polypeptide. When many amino acids strung together interact with each other to form a properly folded molecule, we call that molecule a protein.

For a string of amino acids to ultimately fold up into an active protein, they must first be assembled in the correct order. The code for their assembly lies in the DNA, but once that code has been read and the amino acid chain built, we call that simple, unfolded chain the primary structure of the protein.

This chain can consist of hundreds of amino acids that interact all along the sequence. Some amino acids are hydrophobic and some are hydrophilic. In this context, like interacts best with like, so the hydrophobic amino acids will interact with one another, and the hydrophilic amino acids will interact together. As these contacts occur along the string of molecules, different conformations will arise in different parts of the chain. We call these different conformations along the amino acid chain the protein’s secondary structure.

Once those interactions have occurred, the protein can fold into its final, or tertiary structure and be ready to serve as an active participant in cellular processes. To achieve the tertiary structure, the amino acid chain’s secondary interactions must usually be ongoing, and the pH, temperature, and salt balance must be just right to facilitate the folding. This tertiary folding takes place through interactions of the secondary structures along the different parts of the amino acid chain.

The final product is a properly folded protein. If we could see it with the naked eye, it might look a lot like a wadded up string of pearls, but that “wadded up” look is misleading. Protein folding is a carefully regulated process that is determined at its core by the amino acids in the chain: their hydrophobicity and hydrophilicity and how they interact together.

In many instances, however, a complete protein consists of more than one amino acid chain, and the complete protein has two or more interacting strings of amino acids. A good example is hemoglobin in red blood cells. Its job is to grab oxygen and deliver it to the body’s tissues. A complete hemoglobin protein consists of four separate amino acid chains all properly folded into their tertiary structures and interacting as a single unit. In cases like this involving two or more interacting amino acid chains, we say that the final protein has a quaternary structure. Some proteins can consist of as many as a dozen interacting chains, behaving as a single protein unit.

A Plethora of Purposes

What does a protein do? Let us count the ways. Really, that’s almost impossible because proteins do just about everything. Some of them tag things. Some of them destroy things. Some of them protect. Some mark cells as “self.” Some serve as structural materials, while others are highways or motors. They aid in communication, they operate as signaling molecules, they transfer molecules and cut them up, they interact with each other in complex, interrelated pathways to build things up and break things down. They regulate genes and package DNA, and they regulate and package each other.

As described above, proteins are the final folded arrangement of a string of amino acids. One way we obtain these building blocks for the millions of proteins our bodies make is through our diet. You may hear about foods that are high in protein or people eating high-protein diets to build muscle. When we take in those proteins, we can break them apart and use the amino acids that make them up to build proteins of our own.

Nucleic Acids

How does a cell know which proteins to make? It has a code for building them, one that is especially guarded in a cellular vault in our cells called the nucleus. This code is deoxyribonucleic acid, or DNA. The cell makes a copy of this code and send it out to specialized structures that read it and build proteins based on what they read. As with any code, a typo–a mutation–can result in a message that doesn’t make as much sense. When the code gets changed, sometimes, the protein that the cell builds using that code will be changed, too.

Biohazard!The names associated with nucleic acids can be confusing because they all start with nucle-. It may seem obvious or easy now, but a brain freeze on a test could mix you up. You need to fix in your mind that the shorter term (10 letters, four syllables), nucleotide, refers to the smaller molecule, the three-part building block. The longer term (12 characters, including the space, and five syllables), nucleic acid, which is inherent in the names DNA and RNA, designates the big, long molecule.

DNA vs. RNA: A Matter of Structure

DNA and its nucleic acid cousin, ribonucleic acid, or RNA, are both made of the same kinds of building blocks. These building blocks are called nucleotides. Each nucleotide consists of three parts: a sugar (ribose for RNA and deoxyribose for DNA), a phosphate, and a nitrogenous base. In DNA, every nucleotide has identical sugars and phosphates, and in RNA, the sugar and phosphate are also the same for every nucleotide.

So what’s different? The nitrogenous bases. DNA has a set of four to use as its coding alphabet. These are the purines, adenine and guanine, and the pyrimidines, thymine and cytosine. The nucleotides are abbreviated by their initial letters as A, G, T, and C. From variations in the arrangement and number of these four molecules, all of the diversity of life arises. Just four different types of the nucleotide building blocks, and we have you, bacteria, wombats, and blue whales.

RNA is also basic at its core, consisting of only four different nucleotides. In fact, it uses three of the same nitrogenous bases as DNA–A, G, and C–but it substitutes a base called uracil (U) where DNA uses thymine. Uracil is a pyrimidine.

DNA vs. RNA: Function Wars

An interesting thing about the nitrogenous bases of the nucleotides is that they pair with each other, using hydrogen bonds, in a predictable way. An adenine will almost always bond with a thymine in DNA or a uracil in RNA, and cytosine and guanine will almost always bond with each other. This pairing capacity allows the cell to use a sequence of DNA and build either a new DNA sequence, using the old one as a template, or build an RNA sequence to make a copy of the DNA.

These two different uses of A-T/U and C-G base pairing serve two different purposes. DNA is copied into DNA usually when a cell is preparing to divide and needs two complete sets of DNA for the new cells. DNA is copied into RNA when the cell needs to send the code out of the vault so proteins can be built. The DNA stays safely where it belongs.

RNA is really a nucleic acid jack-of-all-trades. It not only serves as the copy of the DNA but also is the main component of the two types of cellular workers that read that copy and build proteins from it. At one point in this process, the three types of RNA come together in protein assembly to make sure the job is done right.


 By Emily Willingham, DXS managing editor 
This material originally appeared in similar form in Emily Willingham’s Complete Idiot’s Guide to College Biology