Category Archives: Life Science

People are Superorganisms With Microbiomes of Thousands of Species

In a recent article in National Geographic Carl Zimmer has again done a good job of explaining the complex interaction between our bodies and the bacteria and microbes that make us sick, and keep us healthy.

The damage done by our indiscriminate use of antibiotics is not just the long term resistance that we create in bacteria (making the future more dangerous for people) that I have written about numerous times but it also endangers the person taking the anti-biotics in the short term. Sometimes the other damage is a tradeoff that should be accepted. But far too often we ignore the damage taking antibiotics too often does.

When You Swallow A Grenade

While antibiotics can discriminate between us and them, however, they can’t discriminate between them and them–between the bacteria that are making us sick and then ones we carry when we’re healthy. When we take a pill of vancomycin, it’s like swallowing a grenade. It may kill our enemy, but it kills a lot of bystanders, too.
…
If you think of the human genome as all the genes it takes to run a human body, the 20,000 protein-coding genes found in our own DNA are not enough. We are a superorganism that deploys as many as 20 million genes.
…
Before he started taking antibiotics, the scientists identified 41 species in a stool sample. By day 11, they only found 13. Six weeks after the antibiotics, the man was back up to 38 species. But the species he carried six weeks after the antibiotics did not represent that same kind of diversity he had before he took them. A number of major groups of bacteria were still missing.
…
They found that children who took antibiotics were at greater risk of developing inflammatory bowel disease later in life. The more antibiotics they took, the greater the risk. Similar studies have found a potential link to asthma as well.

The human body contains trillions of microorganisms — outnumbering human cells by 10 to 1. Because of their small size, however, microorganisms make up only about 1% to 3% of the body’s mass, but play a vital role in human health.

Where doctors had previously isolated only a few hundred bacterial species from the body, Human Microbiome Project (HMP) researchers now calculate that more than 10,000 microbial species occupy the human ecosystem. Moreover, researchers calculate that they have identified between 81% and 99% of all microorganismal genera in healthy adults.

“Humans don’t have all the enzymes we need to digest our own diet,” said Lita Proctor, Ph.D., NHGRI’s HMP program manager. “Microbes in the gut break down many of the proteins, lipids and carbohydrates in our diet into nutrients that we can then absorb. Moreover, the microbes produce beneficial compounds, like vitamins and anti-inflammatories that our genome cannot produce.” Anti-inflammatories are compounds that regulate some of the immune system’s response to disease, such as swelling.

“Enabling disease-specific studies is the whole point of the Human Microbiome Project,” said Barbara MethÃ©, Ph.D., of the J. Craig Venter Institute, Rockville, MD, and lead co-author of the Nature paper on the framework for current and future human microbiome research. “Now that we understand what the normal human microbiome looks like, we should be able to understand how changes in the microbiome are associated with, or even cause, illnesses.”

Read the full NIH press release on the normal bacterial makeup of the body

Human Gene Origins: 37% Bacterial, 35% Animal, 28% Eukaryotic

The percent of human genes that emerged in various stages of evolution: 37% bacterial, 28% eukaryotic, 16% animal, 13% vertebrate, 6% primate. The history that brought us to where we are is amazing. Eukaryotes include animals, plants, amoebae, flagellates, amoeboflagellates, fungi and plastids (including algae). So eukaryotic genes are those common to us and other non-animal eukaryotes while those classified as animal genes are shared by animals but not non-animal eukaryotes.

We are living in a bacterial world, and it’s impacting us more than previously thought by Lisa Zyga

Bacterial signaling is not only essential for development, it also helps animals maintain homeostasis, keeping us healthy and happy. As research has shown, bacteria in the gut can communicate with the brain through the central nervous system. Studies have found that mice without certain bacteria have defects in brain regions that control anxiety and depression-like behavior. Bacterial signaling also plays an essential role in guarding an animal’s immune system. Disturbing these bacterial signaling pathways can lead to diseases such as diabetes, inflammatory bowel disease, and infections. Studies also suggest that many of the pathogens that cause disease in animals have “hijacked” these bacterial communication channels that originally evolved to maintain a balance between the animal and hundreds of beneficial bacterial species.
…
Scientists have also discovered that bacteria in the human gut adapts to changing diets. For example, most Americans have a gut microbiome that is optimized for digesting a high-fat, high-protein diet, while people in rural Amazonas, Venezuela, have gut microbes better suited for breaking down complex carbohydrates. Some people in Japan even have a gut bacterium that can digest seaweed. Researchers think the gut microbiome adapts in two ways: by adding or removing certain bacteria species, and by transferring the desired genes from one bacterium to another through horizontal gene transfer. Both host and bacteria benefit from this kind of symbiotic relationship, which researchers think is much more widespread than previously thought.
…
We want badly for the message in ‘Animals in a bacterial world,’ to be a call for the necessary disappearance of the old boundaries between life science departments (e.g., Depts of Zoology, Botany, Microbiology, etc.) in universities, and societies (e.g., the American Society for Microbiology, etc.). We also want the message disseminated in college and university classes from introductory biology to advanced courses in the various topic areas of our paper.”

Very cool stuff. This amazing facts scientists discover provide an amazing view of the world we live in and how interconnected we are to other life forms in ways we don’t normally think of.

How Corn Syrup Might Be Making Us Fat

How Corn Syrup Might Be Making Us Hungry–and Fat by Katherine Harmon

…Glucose lowered the activity of the hypothalamus but fructose actually prompted a small spike to this area. As might be expected from these results, the glucose drink alone increased the feelings of fullness reported by volunteers, which indicates that they would be less likely to consume more calories after having something sweetened with glucose than something sweetened with more fructose.

Fructose and glucose look similar molecularly, but fructose is metabolized differently by the body and prompts the body to secrete less insulin than does glucose (insulin plays a role in telling the body to feel full and in dulling the reward the body gets from food). Fructose also fails to reduce the amount of circulating ghrelin (a hunger-signaling hormone) as much as glucose does. (Animal studies have shown that fructose can, indeed, cross the blood-brain barrier and be metabolized in the hypothalamus.) Previous studies have shown that this effect was pronounced in animal models…

Most of the science indicates calories consumed is by far the dominant factor in weight gain. Different foods with the same calories can affect how hungry you feel. Thus the biggest factor in reducing weight gain seems to be reducing calories and one way to help is to eat food that leaves you feeling full and avoid foods that don’t.

The science is not completely clear though on whether certain diets can have a significant affect above and beyond calorie levels. I am skeptical of such claims, however. There are concerns beyond calories for healthy eating – getting a well balanced diet is important.

Healthy physical activity is also important. Burning off calories with exercise allows more consumption without weight gain. And exercise is important for health not just to avoid gaining weight.

Drug Company Funding Taints Published Medical Research

Science provide the opportunity for us to achieve great benefits for society. However, especially in medical research money can make what are already very difficult judgments even less reliable. Add that to a very poor understanding of science in those we elect and you have a dangerous combination. That combination is one of the largest risks we face and need to manage better. I wish we would elect people with a less pitiful appreciation for science but that doesn’t seem likely. That makes doing a better job of managing the conflicts of interest money puts into our current medical research a top priority.

How Drug Company Money Is Undermining Science by Charles Seife

In the past few years the pharmaceutical industry has come up with many ways to funnel large sums of money—enough sometimes to put a child through college—into the pockets of independent medical researchers who are doing work that bears, directly or indirectly, on the drugs these firms are making and marketing. The problem is not just with the drug companies and the researchers but with the whole system—the granting institutions, the research labs, the journals, the professional societies, and so forth. No one is providing the checks and balances necessary to avoid conflicts.
…
Peer-reviewed journals are littered with studies showing how drug industry money is subtly undermining scientific objectivity. A 2009 study in Cancer showed that participants somehow survived longer when a study’s authors had conflicts of interest than when the authors were clean. A 1998 study in the New England Journal of Medicine found a “strong association” between researchers’ conclusions about the safety of calcium channel blockers, a class of drugs used to reduce blood pressure, and their financial relationships with the firms producing the drugs.

Most of those in the system have an interest in minimizing an effort to clean this up. It is just more work they don’t want to do. Or it goes directly against their interest (drug companies that want to achieve favorable opinions by buying influence). The main political message in the USA for a couple decades has been to reduce regulation. Allowing research that is tainted because you find regulation politically undesirable is a bad idea. People that understand science and how complex medical research is appreciate this.

Sadly when we elect people that by and large are scientifically illiterate they don’t understand the risks of the dangerous practices they allow. Even if they were scientifically illiterate but understood their ignorance they could do a decent job by getting scientific consultation from experts but they don’t (to an extent they listen to the scientists that those that give them lots of money tell them to which does help make sure those giving the politicians cash have their interests served but it is not a good way to create policy with the necessary scientific thinking needed today).

Parrots Given “Names” by Their Parents and Use Them Throughout Their Lives

Parrots learn their ‘names’ from their parents

Parrots, which have long amused us for their ability to imitate our vocal patterns, actually learn to caw their “names” from their parents, says a new Cornell study. The research offers the first evidence that parrots learn their unique signature calls from their parents and shows that vocal signaling in wild parrots is a socially acquired rather than a genetically wired trait.
…
Previous research had shown that all wild parrots use unique “contact calls” that not only distinguish each bird individually, but also communicate their gender, and the mate and larger group they belong to.
…
“Parrots can have extremely long periods [leading up] to independence, and this is thought to be related to their large brains,” explained Berg. The same goes for primates, he said, with humans in particular being “off the charts” when it comes to a lengthy stage of child dependence.

More research is required, to better understand the evolution of and interaction between these physical and behavioral traits, he said. “We still don’t have good explanations of how these behaviors help wild individuals survive and reproduce in nature,” he said.

The paper offers some possible explanations: Perhaps the parrots’ far-ranging journeys to “communal foraging sights” are what impress upon each parent the need to have their fledglings’ names sorted out — not unlike human parents’ need to call for their children by name at a crowded fair.

I enjoy learning more fun and cool stuff about the animals we share the world with. They are quite an interesting bunch of creatures.

How Caffeine Affects Your Body

From the video by Alex Dainis: Caffeine prevents adenosine from slowing down your nervous system, by binding to the same receptors adenosine would. Caffeine also stimulates the production of adrenaline. And it increases the amount of dopamine present. The average half life of caffeine in the human body is about 6 hours.

I have been curious about the caffeine content of various drinks and writing this post is a good enough reason to actually look it up.

expresso (2oz) 100 mg (varies – 60 mg to 180 mg)
coffee (8oz) 100 mg – this can vary quite a bit, 50 to over 100 mg is common. Brewed coffee has more caffeine 100-200 mg.
Red Bull (8.2 oz) 80 mg
tea (8oz) 20 to 80 mg (depending on strength and type, can also be higher, green tea is on the lower end)
Mountain Dew (12 oz) 54 mg (diet has 54 mg also)
Diet Coke 46 mg (regular Coke 34mg)
Pepsi 38 mg, Diet Pepsi 36 mg

Sprite, 7Up and some root beers have no caffeine.
Chocolate can also be a significant source of caffeine – dark chocolate can have over 80 mg per 100 g (approximately 4 ounces).

Cancer Cells in Blind Mole Rats ‘commit suicide’

Cancer cells in blind mole rats ‘commit suicide’

Blind mole rats don’t get cancer, and geneticists have worked out why — their cells kill themselves with a poisonous protein when they multiply too much.

Blind mole rats, which live in underground burrows throughout Southern and Eastern Africa, and the Middle East, are fascinating creatures. The naked mole rat, in particular, is the only cold-blooded mammal known to man, doesn’t experience pain, and is also arguably the only mammal (along with the Damaraland mole rat) to demonstrate eusociality — that is, they live in large hierarchical communities with a queen and workers, like ants or bees.

They’re also cancer-proof, which was found in 2011 to be down to a gene that stops cancerous cells from forming. The same team thought that two other cancer-proof mole rat species might have similar genes, but instead it turns out that they do develop cancerous cells — it’s just that those cells are programmed to destroy themselves if they become dangerous.

Very interesting research. The results of evolution are amazing. And while turning the medical research discoveries into workable treatments for people is very difficult the continued increase in our knowledge helps us find treatments that work.

Evolution Follows a Predictable Genetic Pattern

Far from random, evolution follows a predictable genetic pattern

The researchers carried out a survey of DNA sequences from 29 distantly related insect species, the largest sample of organisms yet examined for a single evolutionary trait. Fourteen of these species have evolved a nearly identical characteristic due to one external influence — they feed on plants that produce cardenolides, a class of steroid-like cardiotoxins that are a natural defense for plants such as milkweed and dogbane.

Though separated by 300 million years of evolution, these diverse insects — which include beetles, butterflies and aphids — experienced changes to a key protein called sodium-potassium adenosine triphosphatase, or the sodium-potassium pump, which regulates a cell’s crucial sodium-to-potassium ratio. The protein in these insects eventually evolved a resistance to cardenolides, which usually cripple the protein’s ability to “pump” potassium into cells and excess sodium out.
…
Andolfatto and his co-authors examined the sodium-potassium pump protein because of its well-known sensitivity to cardenolides. In order to function properly in a wide variety of physiological contexts, cells must be able to control levels of potassium and sodium. Situated on the cell membrane, the protein generates a desired potassium to sodium ratio by “pumping” three sodium atoms out of the cell for every two potassium atoms it brings in.

Cardenolides disrupt the exchange of potassium and sodium, essentially shutting down the protein, Andolfatto said. The human genome contains four copies of the pump protein, and it is a candidate gene for a number of human genetic disorders, including salt-sensitive hypertension and migraines. In addition, humans have long used low doses of cardenolides medicinally for purposes such as controlling heart arrhythmia and congestive heart failure.

Cool stuff. It makes sense to me which is nice (it is nice to get confirmation that I find what actually exists is sensible). When things that are true just seem crazy it is a bit disconcerting – like quantum mechanics. It is fun to read stuff that totally shakes up preconceived notions, but even then it is nice once I think understand it to find it sensible.

Does Diet Soda Result in Weight Gain?

Most of us want medical studies to provide clearer (more certain, more specific, more universal) indications than they actually provide. The conclusion of medical studies are often very clouded. Each person has a myriad of complex factors effecting how nutrition, activity and medication will affect us. Certain general conclusion can be drawn but it is very complex and difficult to universally state without various equivocations.

Advice For Diet Soda Lovers: Skip The Chips

Researchers at the University of North Carolina-Chapel Hill found that diet soda drinkers who ate a so-called “prudent” diet, rich in fruit, fish, vegetables, whole grains, nuts and milk, were significantly less likely to develop metabolic syndrome over 20 years than those who ate a “Western diet” heavy in fried foods, meats and sugars.

Metabolic syndrome is a condition characterized by excess abdominal fat, elevated blood sugar, high blood pressure, elevated triglycerides and low HDL cholesterol. About 32 percent of the participants in the “Western diet” cluster developed the condition.

The question of whether diet soda truly helps people manage their weight turns out to be a very tough one to answer.

Conflicting findings abound. A large study published in the New England Journal of Medcine last year found that diet soda had no effect on weight. But another one, published in 2008, found that drinking more than three diet drinks a day led to weight gain.

I would like to know, with much greater certainty what nutritional and food related advice I need to consider when making my choices. To a significant degree I think there is going to be quite a bit of uncertainty (much more than we want) for at least the next 30 years (projecting far out into the future with any accuracy seems very difficult to me.

I am skeptical of purely correlational results. You can try to have similar subsets of people but that is actually hard and if you allow for similar groups and then let the choose something (like diet sodas or not) the chance of that actually being a significant choice that results in many other decisions being different between the subgroups seems a big risk (that makes accepting the correlation as evidence as risky). When you have a scientific explanation it makes the evidence much more compelling, but it is also easy to be taken in by explanations meant to fit the results of a study.

I can believe diet soda can do some bad things to your health. I believe if you are trying to reduce your weight by reducing calories drinking diet soda in place of sugary soda is a big help. I can believe drinking water instead of diet soda would be even better. I want caffeine and don’t like coffee. I have cut down drinking Mountain Dew to less than 2 a week. I have substituted diet soda over the last year. I am not sure that is the right choice, but it is the one I have made so far.

Medical Studies Showing Largest Benefits Often Prove to be False

There is another study showing the results of health studies often are proven false. Medical studies with striking results often prove false

If a medical study seems too good to be true, it probably is, according to a new analysis.

In a statistical analysis of nearly 230,000 trials compiled from a variety of disciplines, study results that claimed a “very large effect” rarely held up when other research teams tried to replicate them.
…
The report should remind patients, physicians and policymakers not to give too much credence to small, early studies that show huge treatment effects, Ioannidis said.

The Stanford professor chose to publish this paper in a closed science publication. But previously he published openly on: Why Most Published Research Findings Are False.