Article: Genetically engineered yeast produces opioids

It typically takes a year to produce hydrocodone from plants, but scientistst have now genetically modified yeast to make it in just a few days. The technique could improve access to medicines in impoverished nations, and later be used to develop treatments for other diseases. 

After a decade's work a team led by Stanford bioengineer Christina Smolke succeeded in finding more than 20 genes from five different organisms and engineering them into the genome of baker's yeast. In so doing they created two different microbial assembly lines, each of which took less than five days to convert sugar into one of two medicinal compounds: either thebaine, which can be refined into painkillers, or hydrocodone which is a prescription painkiller.

My first thought is, "Great! No more dependence on poppy growers in war-torn parts of the world. Poppy plants can be eradicated without a problem."

My second thought is, "Oh, no! Anyone who can make beer can now make opioids."

Article: Airplane Poop Could Help Track Global Disease Outbreaks

IN THE SUMMER of 2013, researchers at the Technical University of Denmark headed to the Copenhagen airport for a special delivery: poop. The crew who clean out airplane toilets had siphoned it from flights arriving from around the world just for them. 

Back in the lab, the researchers turned the samples into DNA soup and fed them through a sequencing machine. Out the other end came antimicrobial resistance genes and potential pathogens—all traceable to the individual plane’s country of origin.

[snip]

From the airplane waste, the Danish researchers could identify regional patterns. Genes for antimicrobial resistance, for example, were more abundant in samples from South Asia than North America. They found differences in specific bacteria, too: Salmonella enterica, which can cause diarrhea, was more common in South Asian samples while Clostridium difficile, the bacteria behind a difficult-to-treat hospital-acquired infection that often follows a course of antibiotics, was most common in North American samples. 

Article: Genes influence academic ability across all subjects, latest study shows [Update: Eugenics 2.0]

Around 60% of differences in GCSE results can be explained by genetic factors, with the same genes responsible for maths, science and the humanities 

The study suggests that a weakness in one subject is most likely to be caused by environmental factors, such as teaching, as the genes affecting ability for different subjects are the same. 

Results in all subjects, including maths, science, art and humanities, were highly heritable, with genes explaining a bigger proportion of the differences between children (54-65%) than environmental factors, such as school and family combined (14-21%), which were shared by the twins.

The article linked below suggests that inheritability of homosexuality is about about 35%; or, in other words, about half the inheritabilty of academic ability (including intelligence, memory, diligence, and curiosity).

I found this article in a post I will not link to. One of the points that the author makes is that "eugenics 2.0" is inevitable. Eugenics 2.0 will target the bearers of specific genes; for example, those involved in violence or low academic ability. While there will be a disparate impact in terms of race and ethnicity, eugenics 2.0 advocates will be able to declare that their motivation will not be racism. Eugenics 1.0, an enterprise of early 20th century Progressives, openly advocated sterilizing of the "unfit" and controlling the population of inferior races. Eugenics 2.0 will not have to and still acheive the same result.

Update: National Security Will Drive Genetically Enhanced Offspring

Eugene Volokh thinks the US will feel pressure to allow offspring IQ boosting or fall behind other nations. It becomes a national security issue if the American population becomes 20 IQ points lower than China, India, and Russia. So expect the national wing of a nation's elites to promote offspring genetic engineering. 

In spite of the outliers I expect offspring genetic engineering will lead to brighter, better looking, higher performing, and healthy children and adults. What I'm less sure about is personality traits and moral reasoning circuitry.  

[snip] 

Then the rate of human evolution will skyrocket. We live in the final decades of human wild type. Some day wild type humans will be the minority. In some countries that will happen in this century.

Article: The association between intelligence and lifespan is mostly genetic

Background: Several studies in the new field of cognitive epidemiology have shown that higher intelligence predicts longer lifespan. This positive correlation might arise from socioeconomic status influencing both intelligence and health; intelligence leading to better health behaviours; and/or some shared genetic factors influencing both intelligence and health. Distinguishing among these hypotheses is crucial for medicine and public health, but can only be accomplished by studying a genetically informative sample.

A long standing, and powerful, assumption among many people is that human beings are born as a "blank slate" and that any differences in outcomes among individuals or various socioeconomic groups must be due to disadvantages and oppression. This is another nail in the coffin of that pernicious paradigm.

Key Messages

• It has been reported that brighter people live longer; we asked ‘why?'.
• We found, using data from three studies, that the small association between being brighter and living longer was mostly genetic in origin.
• This is a key finding in cognitive epidemiology; it is a further indication that intelligence is not just ‘school-smarts'.

I like this also because it shows the scientific method in operation.

Observation: Brighter people live longer.
Problem: Why do brighter people live longer?
Hypotheses: This positive correlation might arise from
1. socioeconomic status influencing both intelligence and health;
2. intelligence leading to better health behaviours;
3. and/or some shared genetic factors influencing both intelligence and health.
Experiment: retrospective analysis of three, long-term twin studies
Results: a small association between intelligence and living longer is mostly genetic in origin.
Conclusion: "intelligence is not just ‘school-smarts'."

Hypothesis falsification:
Factoring in socioeconomic factors, and health behaviors, using data from Sweden, seems to indicate that these factors do not influence lifespan.

In other word, environmental factors have a smaller effect on life span than genetic factors, such as intelligence.

Article: Male sexual orientation influenced by genes, study shows

A study of gay men in the US has found fresh evidence that male sexual orientation is influenced by genes. Scientists tested the DNA of 400 gay men and found that genes on at least two chromosomes affected whether a man was gay or straight. 

A region of the X chromosome called Xq28 had some impact on men's sexual behaviour – though scientists have no idea which of the many genes in the region are involved, nor how many lie elsewhere in the genome. 

Another stretch of DNA on chromosome 8 also played a role in male sexual orientation – though again the precise mechanism is unclear.

The cause of homosexuality in males is a fraught subject. There are, basically, three possible causes: free choice, genetic determination, and envirnmental factors.

Most male homosexuals say that, looking back, they knew they were homosexuals from an early age based on what and who attracted them. And they reject the idea that they chose a homosexual orientation.

It is obvious from previous studies on twins, going back to the 1980's, that there is a genetic component to male homosexuality, although there is not a 1:1 correlation with genes and homosexuality as there is with genes for eye color or (most) hair colors.  It is much lower.

Wikipedia: Biometric modeling revealed that, in men, genetic effects explained .34–.39 of the variance [of sexual orientation], the shared environment .00, and the individual-specific environment .61–.66 of the variance. 

In other words, while genetics plays a factor causing male homosexuality, its effect is half the size of enviornmental factors, whatever they may be.

The flawed thinking behind a genetic test for sexual orientation is clear from studies of twins, which show that the identical twin of a gay man, who carries an exact replica of his brother's DNA, is more likely to be straight than gay. 

A very clear example of the larger effect of environmental factors.

Article: Rise in Autism May Be Due to Semantics, Study Finds

Autism, autism-spectrum disorder, and Asperger's syndrome. 

A new study suggests the idea that more kids are being diagnosed with autism not because something catastrophic has happened to U.S. children, but rather because they're simply being classified and diagnosed differently.

Special education enrollment figures suggest 97 percent of the increase in autism seen between 2000 and 2010 could simply be accounted for by reclassification — at least among older kids — a team at Penn State University found. [And about 2/3 of the total increase.]

[snip] 

Santhosh Girirajan, an assistant professor of biochemistry and molecular biology and of anthropology at Penn State and colleagues looked at 11 years of special-education enrollment data covering more than 6 million children a year. They found that the increase in students designated as having autism could be offset by a nearly equal decrease in students diagnosed with other intellectual disabilities often seen along with autism.

Additionally, higher autism rates are found in children of teen parents and of older parents. Since there has been more of those two groups over the last 30 years or so, that could account for some of the rest of the increase. 

Also, there is a genetic factor at work as well. Parents who are detailed oriented tend to be at an increased risk of having children with autism. It used to be that men who were detailed oriented tended to end up certain occupations, such as engineering. Women in others. These men would tend to find spouses at church or in social organizations or in support staff where they worked. These women would be less likely to carry any autism related genes. 

Because detail-oriented women are being encouraged to move into engineering type occupations, detail oriented men and women are now  more likely to marry each other. This increases the risk of a "double dose" of the genes related to autism. 

If these three things are true, they probably account for close to 100% of the increase in the diagnosis of autism and its related syndromes. 

Article: How your brain reacts to emotional information is influenced by your genes

One long standing cultural conflict is between the idea that humans are a blank slate and the idea that humans have a recognizable "human nature."

The "blank slate" idea is the idea, more common on the political left, that humans have no single basic nature and that any evil they do is because they have been corrupted by (usually Western) culture. 

The "human nature" idea is the idea, more common on the political right, that humans have a "hard-wired" nature that can only be modified by upbringing and that has both good and evil aspects. 

Orthodox Christianity holds that all humans have a "fallen" nature that is less than perfect and is corrupt by nature, even if all humans are capable of good. 

Marism explicitly accepts the blank slate idea. One of the outworkings of this idea is that there are no inherent differences between classes, sexes, races, or ethnic groups. Therefore, any apparent differences are due to oppression by the dominant group. For example, a lack of female scientists is soley due to the dominant group, men, keeping women out, rather than a lack of women trying to get in. 

Your genes may influence how sensitive you are to emotional information, according to new research by a neuroscientist. The study found that carriers of a certain genetic variation perceived positive and negative images more vividly, and had heightened activity in certain brain regions.

Or, paraphrased, your genes influence how much empathy you show. People who have a specific gene react more strongly to emotions and that this reaction is hard-wired into your brain. 

"People really do see the world differently," says lead author Rebecca Todd, a professor in UBC's Department of Psychology. "For people with this gene variation, the emotionally relevant things in the world stand out much more." 

[snip] 

Todd believes this may help explain why some people are more susceptible to PTSD and intrusive memories following trauma. 

[snip] 

The ADRA2b deletion variant appears in varying degrees across different ethnicities. Although roughly 50 per cent of the Caucasian population studied by these researchers in Canada carry the genetic variation, it has been found to be prevalent in other ethnicities. For example, one study found that just 10 per cent of Rwandans carried the ADRA2b gene variant.

In other words, Caucasians are much more likely to be attuned to the emotional states of others than Rwandans. This raises the question how common is this gene variant in other populations? 

Other implications: 

ADRA2b insertion variant appears to be correlated with hypertention, but inversersely correlated with type 2 diabetes in ethnic Han Chinese men. 

Evolution rates and DNA mutation clocks

Article: DNA mutation clock proves tough to set

I don't want to get into the weeds about this. I have seen some triumphalism among the more Bible-believing sites I visit that this disproves the possibility that everything evolved without any "outside" interference [read: God]. Or at least calls into a completely atheistic view of evolution.

I am not so certain.

Mathematicians keep refining π even though they know it to more than 12 trillion digits; physicists beat themselves up because they cannot pin down the gravitational constant beyond three significant figures. Geneticists, by contrast, are having trouble deciding between one measure of how fast human DNA mutates and another that is half that rate.

Or another way of putting that, "and another that is twice that rate."

Mutations provide the raw material for evolution. Red, blond and brown hair colors are the result of mutations. The ability in adult humans to digest milk and milk products is the result of a mutation.

The rate is key to calibrating the ‘molecular clock’ that puts DNA-based dates on events in evolutionary history. 

How fast genes mutate determine how fast evolution can happen. If the rate is too slow, then life could not have originated and evolved into it current diversity in the time allowed.

A slower molecular clock worked well to harmonize genetic and archaeological estimates for dates of key events in human evolution, such as migrations out of Africa and around the rest of the world. But calculations using the slow clock gave nonsensical results when extended further back in time — positing, for example, that the most recent common ancestor of apes and monkeys could have encountered dinosaurs. 

"Slow clock." "Fast clock." "Dinosaurs."

Reluctant to abandon the older numbers completely, many researchers have started hedging their bets in papers, presenting multiple dates for evolutionary events depending on whether mutation is assumed to be fast, slow or somewhere in between.

Evolution works on the gene variations that are present in a population. Mutations provide those variations. One cannot speed up evolution in a population that does not have sufficient variations to change.

"Hedging their bets." Using different estimates to fit the data is the wrong way round of doing things. One takes the data and have it drive the estimates, guesses, and hypotheses.

The biological transmission of memory.

Article: Phobias may be memories passed down in genes from ancestors

In the study, which is published in the journal of Nature Neuroscience, the researchers trained mice to fear the smell of cherry blossom using electric shocks before allowing them to breed. 

The offspring produced showed fearful responses to the odour of cherry blossom compared to a neutral odour, despite never having encountered them before. 

The following generation also showed the same behaviour. This effect continued even if the mice had been fathered through artificial insemination.The researchers found the brains of the trained mice and their offspring showed structural changes in areas used to detect the odour.

Up until recently, this would have been considered nonsense. Classical evolution and genetics stated that the experiences of the parent could not be transmitted to offspring. At its most extreme, evolution was seen as favoring only those genes that were most successful in passing themselves onto offspring. Genes could affect behavior, but not the other way around.

The DNA of the animals also carried chemical changes, known as epigenetic methylation, on the gene responsible for detecting the odour. 

This suggests that experiences are somehow transferred from the brain into the genome, allowing them to be passed on to later generations. 

The researchers now hope to carry out further work to understand how the information comes to be stored on the DNA in the first place. 

They also want to explore whether similar effects can be seen in the genes of humans.

We now know that this mechanism exists, though not how it works. How does changes in the brain change the DNA in cells of the ovary and testes that become eggs and sperm?

He added: "It addresses constitutional fearfulness that is highly relevant to [human] phobias, anxiety and post-traumatic stress disorders, plus the controversial subject of transmission of the ‘memory’ of ancestral experience down the generations.

Article: The Science of Why Beer Is So Delicious

So, during its production, the yeast in the beer makes a variety aromatic compounds that gives the beer its distinctive flavors.

Why?

Well, for mostly the same reason that flowers make scents.

The scents attract fruit flies that carry the yeast from one place to another.

Science Links: 10/2/14 [Updated and bumped]

Article: 'Strikingly Geometric' Shapes Hidden on Moon's Surface

A new lunar probe has detected filled-in rift valleys on the moon.

Rifting was first discovered on Earth. Once it was studied and explained, examples on Mars and Venus became obvious.

The Moon, however, was heavily bombarded during its early history. This covered up the more "rectangular" shape of the rifting. The bombardment make the area appear more circular, as if a large asteroid had caused it.

The conclusion would be that some of plate tectonics happened all four of these.

Article: Walrus mass on Alaska beach - in pictures

Pacific walrus unable to find sea ice on which to rest in Arctic waters are coming ashore in record numbers on a beach in north-west Alaska. Females give birth on sea ice and the animals use it as a diving platform to reach snails, clams and worms on the shallow continental shelf, but climate change means there is ever less available.

Cool photos; stupid comment.

Arctic sea ice is up, overall. Any lack of it in the Alaskan area is a local phenomenon due to the way sea ice shifts around the Arctic Ocean.

Update: Walrus Beach Party 

Confirmation of my assumption above. These mass haul-outs are common, and have occurred whether or not there is sea ice in the vicinity or not. Another hysterical over-reaction by ignorant people to a normal event.

Article: Your nose knows death is imminent: Losing the sense of smell predicts death within five years, according to new research

The title is wrong. In elderly people, about 40% of the people who had a measurable loss of the sense of smell died within 5 years. So, no, "your nose does [not] know" anything.

This compares to about 10% of those with a healthy sense of smell.

Senescence: "the gradual deterioration that occurs with age." The sense of smell is probably a proxy for that general deterioration.

And definitely warrants further study.

Article: What causes paranoia, hallucinations and grandiose ideas?

Led by Dr Angelica Ronald at Birkbeck, University of London, the team analysed data on almost 5,000 pairs of 16-year-old twins. This is the classical twin design, a standard method for gauging the relative influence of genes and environment.
Heritability for paranoia was 50%; for grandiosity it was 44%; while for hallucinations it was 15% for males and 32% for females. This doesn’t mean, incidentally, that 50% of an individual’s paranoia is the result of their genes. The concept of “heritability” tells us that 50% of the differences in levels of paranoia across the population may be genetic in origin. 

That would mean that 50% of that difference is environmental (or "nurture") in origin.

The individual symptoms do not necessarily co-occur with one another.

However, these are generally symptoms of schizophrenia, and "twin studies of those diagnosed with schizophrenia typically report much higher rates of heritability for the disorder…."

Despite the authors's conclusions about the non-inheritability of schizophrenia, it would appear that having all the symptoms, at once, may be the result of having all the genes for the symptoms and therefore, increase the likelihood for full-blown schizophrenia.

They are definitely on the side of redefining schizophrenia, so there may be a bias here against finding for a genetic cause of it.

Article: Epigenetics: genes, environment and the generation game
http://www.theguardian.com/science/2014/sep/07/epigenetics-heredity-diabetes-obesity-increased-cancer-risk

This a longish, review-type article that appears well-balanced. It is a very new field with lots of implications for humans. However, epigenetics in mammals in general and humans in particular is controversial.

As with so much in science, this story owes a lot to mice. The tale begins with a pregnant mouse in a laboratory in Boston, Massachusetts. Such is the unfortunate lot of a lab rodent that she was kept on a near-starvation diet when she was close to giving birth. As scientists expected, her babies were born smaller than usual. When they were raised normally, they later developed diabetes. 

Now comes the twist. Even though these mice were well fed, their own young were also born unusually small and with a higher risk of diabetes. This was strange, because nothing had changed genetically and they hadn't suffered any problems in the womb or after they were born. They should have been perfectly healthy. 

There are many definitions of epigenetics, but simply put, says Professor Marcus Pembrey, a geneticist at University College London and the University of Bristol, it is a change in our genetic activity without changing our genetic code. It is a process that happens throughout our lives and is normal to development. Chemical tags get attached to our genetic code, like bookmarks in the pages of a book, signalling to our bodies which genes to ignore and which to use.

What global warming hiatus?

Article: Matt Ridley in the WSJ: Whatever Happened to Global Warming?

The original article is behind a paywall. This link has the complete article.

In effect, this is all that’s left of the global-warming emergency the U.N. declared in its first report on the subject in 1990. The U.N. no longer claims that there will be dangerous or rapid climate change in the next two decades. 

Last September, between the second and final draft of its fifth assessment report, the U.N.’s Intergovernmental Panel on Climate Change quietly downgraded the warming it expected in the 30 years following 1995, to about 0.5 degrees Celsius from 0.7 (or, in Fahrenheit, to about 0.9 degrees, from 1.3). 

Even that is likely to be too high. The climate-research establishment has finally admitted openly what skeptic scientists have been saying for nearly a decade: Global warming has stopped since shortly before this century began.

NASA satellite data from the last 35 years is showing about 1 degree F per century. "If this trend continues" is a logical fallacy. However, 0.9 degrees F per 30 years or 3.0 degrees F per century is way over the current trend.

First the climate-research establishment denied that a pause existed, noting that if there was a pause, it would invalidate their theories. [Ed., yes, they have been invalidated.] Now they say there is a pause (or “hiatus”), but that it doesn’t after all invalidate their theories [magical thinking?]. 

When the climate scientist and geologist Bob Carter of James Cook University in Australia wrote an article in 2006 saying that there had been no global warming since 1998 according to the most widely used measure of average global air temperatures, there was an outcry. A year later, when David Whitehouse of the Global Warming Policy Foundation in London made the same point, the environmentalist and journalist Mark Lynas said in the New Statesman that Mr. Whitehouse was “wrong, completely wrong,” and was “deliberately, or otherwise, misleading the public.” 

We know now that it was Mr. Lynas who was wrong. Two years before Mr. Whitehouse’s article, climate scientists were already admitting in emails among themselves that there had been no warming since the late 1990s. 

Part of what Matt Ridley is describing is a preference cascade. One lonely scientist spoke up (like in the "Emperor's New Clothes" fable) and within a short time, it was acceptable to acknowledge the hiatus was real.

Preference cascade 

As described by Glenn Reynolds in a classic 2002 essay [Patriotism and Preferences], a preference cascade occurs when people trapped inside a manufactured consensus suddenly realize that many other people share their doubts.  Preference falsification works by making doubters feel isolated and alone.  In a totalitarian society, the dissenter fears that if he speaks up, his will be a lone voice, easily squashed by the enforcers of the regime.  When dissenters realize they are not alone, and the true strength of their numbers becomes apparent, “invincible” regimes vanish with astonishing speed.

People will say the thing that causes the least conflict, even if they don't believe it. However, when enough people realize that everyone else (even fellow scientists) are skeptical, the belief system will crash quickly.

It has been roughly two decades since there was a trend in temperature significantly different from zero. The burst of warming that preceded the millennium lasted about 20 years and was preceded by 30 years of slight cooling after 1940.

Other global warming links. 

Article: McKitrick paper: no warming for 19 years

Title says it. Not for the math-faint-of-heart.

Article: Climate Models Show Remarkable Agreement with Recent Surface Warming

...If you throw in a lot of processes that seem to have suddenly become important in the last 20 years, but not before.

People desperate to find global warming, when it is not there, will conjure it out of cold air. "The heat is all there, really! It is just hiding. Watch me find it!"

Maybe I should not scoff, he might be right. However, this is getting close to magical thinking. Why didn't these processes work before the hiatus? If they did work, then there is still a hiatus.

The cause of autism?

Article: Scientists discover people with autism have too many brain 'connections'

As a baby develops, the brain undergoes a burst of synapse formation, the connections between different nerves. Then, over time, these synapses are "pruned" back, retaining the necessary ones.

My guess is that this may be related to why it is easier for someone who hears, and learns to speak, a language when they are young rather than when they are older. The connections are all there, but as someone ages they are lost.

The Columbia University scientists examined the brains of 26 autistic children and young people aged two to 20 who had died from a variety of causes 

By late childhood, the researchers found that spine density had dropped by about half in the healthy brains, but by only 16 per cent in the brains of autistic individuals. 

Lead researcher Professor David Sulzer said: ‘It's the first time that anyone has looked for, and seen, a lack of pruning during development of children with autism, although lower numbers of synapses in some brain areas have been detected in brains from older patients and in mice with autistic-like behaviours.' 

He added: ‘While people usually think of learning as requiring formation of new synapses, the removal of inappropriate synapses may be just as important.

The link between incomes and criminal behavior

Article: A disturbing study of the link between incomes and criminal behaviour

Using the rich troves of personal data which Scandinavian governments collect about their citizens....

Before I get into the article, doesn't this sound a bit creepy?

“POVERTY”, wrote Aristotle, “is the parent of crime.” But was he right? Certainly, poverty and crime are associated. And the idea that a lack of income might drive someone to misdeeds sounds plausible. 

One of the things that I frequently note is that "correlation does mean causation." That is, just because two events occur in tandem does not mean that one causes the other.

First, coincident do happen. And, second, both may be caused by something else entirely.

Using the rich troves of personal data which Scandinavian governments collect about their citizens, Mr Sariaslan and his team were able to study more than half a million children born in Sweden between 1989 and 1993. The records they consulted contained information about these people’s educational attainments, annual family incomes and criminal convictions. They also enabled the researchers to identify everybody’s siblings.

Children, now between 21 and 25 years old. And looking at the behavior of older and younger siblings.

He found, to no one’s surprise, that teenagers who had grown up in families whose earnings were among the bottom fifth were seven times more likely to be convicted of violent crimes, and twice as likely to be convicted of drug offences, as those whose family incomes were in the top fifth.

He showed evidence of the correlation that Aristotle noted 2300 years ago.

What did surprise him was that when he looked at families which had started poor and got richer, the younger children—those born into relative affluence—were just as likely to misbehave when they were teenagers as their elder siblings had been. Family income was not, per se, the determining factor.

So, simply increasing the family's income did not reduce the tendency of criminal behavior in the younger siblings. Why not?

That suggests two, not mutually exclusive, possibilities. One is that a family’s culture, once established, is “sticky”—that you can, to put it crudely, take the kid out of the neighbourhood, but not the neighbourhood out of the kid. Given, for example, children’s propensity to emulate elder siblings whom they admire, that sounds perfectly plausible. 

This is the "nurture" part of the "nature versus nurture" question. Research shows that there seems to be a 50:50 split. That is, about 50% of human behavior seems to be driving by environmental factors, including upbringing.

The other possibility is that genes which predispose to criminal behaviour (several studies suggest such genes exist) are more common at the bottom of society than at the top, perhaps because the lack of impulse-control they engender also tends to reduce someone’s earning capacity.

And the other 50% is due to genetic hardwiring.

Neither of these conclusions is likely to be welcome to social reformers. The first suggests that merely topping up people’s incomes, though it may well be a good idea for other reasons, will not by itself address questions of bad behaviour. 

Throwing money at the problem will not solve the problem.

The second raises the possibility that the problem of intergenerational poverty may be self-reinforcing, particularly in rich countries like Sweden where the winnowing effects of education and the need for high levels of skill in many jobs will favour those who can control their behaviour, and not those who rely on too many chemical crutches to get them through the day. 

Seals, tuberculosis, and DNA

Article: Seals carried tuberculosis across the Atlantic, gave it to humans: Disease was present in the Americas prior to European contact.
This offers a glimpse at the rather complicated history of tuberculosis.

TB leaves recognizable changes in bones. Therefore, it can be the diagnosed from skeletons of the long dead.

In the Old World, the bacteria causing TB made the leap to humans about 10,000 years ago. After that, it made the leap from humans to cattle.

It is known that Native Americans had TB early on. This gave rise to the belief that Westerners brought it to the Americas. However, pre-Columbian skeletons were found showing the disease.

So, if the land bridge from Asia was submerged more than 10,000 years ago, how did the disease get here?

Turns out that bacterial DNA from three, 4,000 year old skeletons of Native Americans in Peru was not the normal, human variant. It was the "pinniped" variation. That is, seals carried TB from Africa to South America, and from there across the Americas.

Seals also carried TB to Australian Aborigines about 700 year ago.

Genes, the hippocampus, and depression

Article: Genes determine traces that stress leaves behind on brains

Our individual genetic make-up determines the effect that stress has on our emotional centers, researchers have found. Not every individual reacts in the same way to life events that produce the same degree of stress. Some grow as a result of the crisis, whereas others break down and fall ill, for example with depression. The outcome is determined by a complex interaction between depression gene versions and environmental factors.

The hippocampus is a switching station in the processing of emotions and acts like a central interface when dealing with stress. It is known to react very sensitively to stress. In situations of stress that are interpreted as a physical danger ('distress'), it shrinks in size, which is a phenomenon observed commonly in patients with depression and one which is responsible for some of their clinical symptoms. By contrast, positive stress ('eustress'), of the kind that can occur in emotionally exciting social situations can actually cause the hippocampus to increase in size.

"People with the three gene versions believed to encourage depression had a smaller hippocampus than those with fewer or none of these gene versions, even though they had the same number of stressful life events," says study leader Lukas Pezawas, describing the results. People with only one or even none of the risk genes, on the other hand, had an enlarged hippocampus with similar life events.

In a previous article posted below, it was noted that 30-40% of a person's risk for depression is genetic. That means that 60-70% of that risk is environmental, also known as "nurture." While some people seem to be "hard-wired" for depression, the 60-70% factor allows for personal choice.

Major factors "protective" against suicide are strong familial and religious relationships. These are free will choices that anyone can make to help protective themselves from suicide, if not from suicidal thoughts.


The depressive thoughts can fight these choices, but they do not have to dominate. There have been articles published recently about how psychiatrists can re-train peoples' thought patterns to overcome some of this thinking.

Microevolution: Pygmies, butterflies, and Tibetans

Three articles about microevolution. That is, the rapid spread of a change in genes through a population because that change confers an advantage to those having the gene.

Article: Pygmy phenotype developed many times, adaptive to rainforest

The small body size associated with the pygmy phenotype is probably a selective adaptation for rainforest hunter-gatherers, according to an international team of researchers. But all African pygmy phenotypes do not have the same genetic underpinning, suggesting a more recent adaptation than previously thought.

Genetic mutations occur in populations all the time. If they have a negative impact on the individual, they tend to disappear from the population quickly. If they have no noticeable impact for the good or bad, they might disappear as well, although more slowly. Mutations which have positive influence on individuals, making them more fit for their environment, tend to spread through the population.

Article: Butterflies' evolutionary responses to warmer temperatures may compromise their ability to adapt to future climate change

Members of the brown argus butterfly species that moved north in response to recent climate change have evolved a narrower diet dependent on wild Geranium plants, researchers report. However, butterflies that did not move north have more diverse diets, including plants such as Rockrose that are abundant in southern parts of the UK.

Article: 8,000-year-old mutation key to human life at high altitudes: Study identifies genetic basis for Tibetan adaptation

In an environment where others struggle to survive, Tibetans thrive in the thin air of the Tibetan Plateau, with an average elevation of 14,800 feet. A new study is the first to find a genetic cause for the adaptation and demonstrate how it contributes to the Tibetans’ ability to live in low oxygen conditions.

About 8,000 years ago, the gene EGLN1 changed by a single DNA base pair. Today, a relatively short time later on the scale of human history, 88% of Tibetans have the genetic variation, and it is virtually absent from closely related lowland Asians. The findings indicate the genetic variation endows its carriers with an advantage.

Genetic testing and suicide

Article: Could a Genetic Test Predict the Risk for Suicide?

A gene test would be invaluable to reducing suicide.

While claims for a suicide test remain preliminary, and controversial, a “suicide gene” is not as fanciful as it sounds. The chance that a person takes his or her own life is in fact heritable, and many scientific teams are now involved in broad expeditions across the human genome to locate suicide’s biological causes.

Based on such gene research, one startup company, Sundance Diagnostics, based in Boulder, Colorado, says it will begin offering a suicide risk test to doctors next month, but only in connection with patients taking antidepressant drugs like Prozac and Zoloft.

The Sundance test rests on research findings reported by the Max Planck Institute of Psychiatry in 2012. The German researchers, based in Munich, scanned the genes of 898 people taking antidepressants and identified 79 genetic markers they claimed together had a 91 percent probability of correctly predicting “suicidal ideation,” or imagining the act of suicide.

So, the first gene test is based on genetic markers. These would be the genes that can be passed on from parents to children. These genes would be part of the basis of the well-known familial risk factor (see below).

Given how many people take antidepressants, the market for a suicide test could be big. In the U.S., about 11 percent of Americans 12 years and older take antidepressants, according to a 2011 estimate by the U.S. Centers for Disease Control and Prevention.

People taking antidepressants have a higher risk of suicidal ideation and suicide. A test would help reduce the risk by identifying those prone to that and getting them counseling in advance of taking the drugs.

Altogether, epidemiologists believe that 30 percent to 55 percent of the risk that someone takes their own life is inherited, and the risk isn’t linked to any specific mental illness, like depression or schizophrenia.

That means suicide probably has its own unique genetic causes....

Oddly enough, a range 30-40% is the same for a lot of conditions that have a genetic linkage: mental illness and heart disease. Even the tendency towards homosexuality.

A person’s life history still has more to do with whether it ends in suicide than genes do. Virginia Willour, a geneticist at the University of Iowa who studies suicidal thinking among bipolar patients, says environmental factors are especially important in preventing suicide. Getting medical treatment, an involved family, and religious beliefs all cut the chance of suicide dramatically.

If 30-40% of the risk for suicide is genetic, then 60-70% of the risk is environmental factors.

The latest report of a possible suicide test came in July from Johns Hopkins University, in Baltimore, where geneticists published a report saying that the presence of alterations to a single gene could predict who will attempt suicide with 80 percent accuracy.

Instead of looking just at DNA, they studied patterns of methylation, a type of chemical block on genes that can lower their activity. They found that one gene, SKA2, seemed to be blocked often in the suicide brains. They later found the same gene block was common when they tested the blood of a larger number of people having suicidal thoughts.

“We seem to be able to predict suicidal behavior and attempts, based on seeing these epigenetic changes in the blood,” says Kaminsky.

Kaminsky says that following the report, his e-mail inbox was immediately flooded by people wanting the test. “They wanted to know, if my dad died from suicide, is my son at risk?” he says. They didn’t understand that the type of DNA change he identified probably isn’t the inherited kind, but instead may be the result of stress or some other environmental factor.

The second test used the DNA from the brains of suicide victims to see if there had been changes to their specific DNA. This would be changes due to environmental factors: chemical and hormonal exposure (including in the womb) or related to stress and life activities. This may account for some of the non-familial risk factors listed below. These changes may or may not be passed on. If they are changes in the brain, only, they will not be. To be passed on, the epigenetic changes would have to also happen in the sex cells (sperm and eggs).

Article: Suicide: Risk and Protective Factors

A combination of individual, relational, community, and societal factors contribute to the risk of suicide. Risk factors are those characteristics associated with suicide—they may or may not be direct causes.

Risk Factors

• Family history of suicide
• Family history of child maltreatment
• Previous suicide attempt(s)
• History of mental disorders, particularly clinical depression
• History of alcohol and substance abuse
• Feelings of hopelessness
• Impulsive or aggressive tendencies
• Cultural and religious beliefs (e.g., belief that suicide is noble resolution of a personal dilemma)
• Local epidemics of suicide
• Isolation, a feeling of being cut off from other people
• Barriers to accessing mental health treatment
• Loss (relational, social, work, or financial)
• Physical illness
• Easy access to lethal methods
• Unwillingness to seek help because of the stigma attached to mental health and substance abuse disorders or to suicidal thoughts

Learning ability and genetics

Article: About half of kids' learning ability is in their DNA, study says

Classic type of twin studies looking at one aspect of intelligence.

Takeaway: Children are not blank slates. While nurture matters it is only, literally, half the story.

Our children are different from each other because the genetic influence is complex. Even small differences in the complex of genes associated with learning ability (and thus intelligence) can add up to a large difference between children.

On the other hand, all of your children are going to be more alike compared to the children of others where the potential mix is going to be different.

You may think you’re better at reading than you are at math (or vice versa), but new research suggests you’re probably equally good (or bad) at both. The reason: The genes that determine a person’s ability to tackle one subject influence their aptitude at the other, accounting for about half of a person’s overall ability.

 If I am more comfortable with math than reading, it may be because I have worked on it more, or take more pleasure in working on it. 

What’s more, the genes responsible for math and reading ability appear to be numerous and interconnected, not specifically targeted toward one set of skills. These so-called “generalist genes” act in concert to determine a child’s aptitude across multiple disciplines.

The finding that one’s propensities for math and reading go hand in hand may come as a surprise to many, but it shouldn’t. People often feel that they possess skills in only one area simply because they perform slightly worse in the other, Plomin said. But it’s all relative.

“You might think you’re a little less good at math, but compared to everybody in the world, you’re pretty good at math,” he said.

“Just as we no longer blame mothers for schizophrenia, we should be humble when blaming schools and parents for not every child learning as quickly as we'd desire,” he said. “The implications, I think, are that children really do differ at very deep levels in how easily they learn.” [Emphasis added.]

I like the emphasis in the article on recognizing hard-wired differences between the abilities of different children.