We crossed the red line and no one noticed

We are confronted with the fierce urgency of now.

(Martin Luther King, April 4, 1967)

The Earth will end when God declares it to be over.

(John Shimkus, Republican congressman, Illinois, chairman of the Subcommittee on Environment and the Economy))

For the sake of our planet, we need to start eating lower down on the food chain and we need to do it fairly soon.

(David George Gordon, science writer)

A story in need of an ending

In case you haven't heard and most likely many haven't, the amount of CO2 in the atmosphere of planet Earth has now risen to 400 parts per million. It's been something like 3 million years since so much carbon dioxide has been hanging over the planet.

The “little-bit” of good news is that 400 ppm is part of a scientific model, a very complex model with a lot of complex parts and poorly understood by most people, which is comforting news to many politicians across the globe. Models of course can be changed, modified or discarded. Unlike the politicians, the scientists could be wrong about a lot or a little and, as some people know, science tries hard to be proven wrong.

The actual “good” news is that we have some idea how to mitigate many of the effects of climate change. For example, in terms of things like deforestation, feed production and animal waste, the

livestock industry produces between 18-51 percent of global greenhouse gas emissions. The industry as well uses a lot of fossil fuels and water.

Could you imagine eating a little less meat? What if you could be persuaded that the future of future generations would quite probably be bleak, unless significant changes were made starting right now? For that matter, the present is feeling a little less certain; we may not need vivid imaginations. For more on this subject see “Additional Reading.”

Genes made me do it—or not

Genetics has come a long way since Gregor Mendel, in the 19^th century, showed how the inheritance of certain traits in pea plants followed particular patterns. Today, with the mapping of the human genome and the ever increasing power of supercomputers, we have arrived at a new scientific Frontier-land. What we do with it is a story searching for a good ending.

I once worked with someone a number of years ago that believed humankind was “d-evolving,” as though the expanding universe showed signs of slowing down and reversing itself. Interestingly, Gerald Crabtree, Professor of Pathology and Developmental Biology at Stamford University, has a fairly controversial view on human intelligence. It's declining, according to Crabtree.

He has said that, “A hunter-gatherer who did not correctly conceive a solution to providing food and shelter probably died, along with his or her progeny, whereas a modern Wall Street executive that made a similar conceptual mistake would receive a substantial bonus and be a more attractive mate.”

Crabtree has suggested that the approximately 5,000 genes, which he believes are the basis for human intelligence, have mutated over the years and modern man is not as intelligent as his ancestors. The professor thinks we may have peaked about 7,000 years ago! At the same time, Crabtree has said that science and technology have allowed us to rise above the “dumbing down.”

Regardless of Professor's Crabtree's thought-provoking ideas, what we know about genes at the present time is quite remarkable. It's not an either or—genetics or environment—it's more like a blending, a mixing and sometimes one is more influential than the other. The answer is frequently that … it depends.

When we're young, environment has a tendency to be more important but when we get older and more independent, genes seem to play a larger role. Certain behaviors, such as criminality, are heritable but only as side effects of genes that affect personality traits. You don't for example have genes for addiction, but you do have genes for impetuosity and risk taking which, under the right environmental circumstances, might lead to addiction.

Neurobiologists have found out that there is a structure in our limbic brain called the amygdala, which causes the feeling of unease. Research has shown that people with larger emotional responses to threats are more likely to have right-wing opinions. There is now a field called Genopolitics, which accepts that political views most likely have a genetic component.

Finally, a little bit of good news to consider. Yes, sex and organisms are healthy, because they release oxytocin, sometimes called the “cuddle hormone.” This particular hormone has the ability to lower amygdala response, which can then increase such traits as generosity and trust. David Buss, a professor of psychology, conducted a “sexual preference study a number of years ago.” He learned that the top two qualities in a mate for both men and women were kindness and intelligence, outweighing things such as money and physical appearance.

Thinking good thought

In summary, how we think, make decisions and frame discussions needs to be understood a lot better. We know now that there is both a genetic and environmental component in decision making, and our survival as a species probably depends on how effectively we can increase the size of who we think belongs in our group. The “clan” is bigger than we think.

Additional Reading:

what to consider

Global carbon dioxide in atmosphere passes milestone level

Bring on the bugs

Would we give up burgers tostop climate change

Entering a resource-shockworld

Frozen Evolution: TheProbability of Extinction

worth reading

How (not) to argue withskeptics and deniers: a historian's guide

Science and Religion Can'tBe Reconciled

Rapid Shifts

Belief in biblical end-timesstifling climate change action in U.S. :study

political hack with a degree in biology

Louisiana counts the cost ofteaching creationism—in reputation and dollars

Remembering uncle Sah

In the beginning

My uncle was different from the others although I was never able to put my finger on it exactly. Sure, he was smarter than most and in some ways he didn't look like everyone else I suppose. Now his eyes, the way he looked at you, as though he knew something you didn't. It was a little spooky at times, but I knew my uncle liked me a lot.

Memories however grow dim, especially after some 7 million years. My uncle's full name is Sahelanthropus (sa-ha-lan-throw-pus) Tchadensis (cha-den-sis), but I've always called him Sah. Scientists, at least for the present, believe he's the best candidate for our last common ancestor with the chimpanzee.

Sah lived in Chad, Africa. Seven million years ago, give or take, was when we diverged from the chimp. We went our separate ways. This is difficult for a lot of humans to accept, how we're all related to Uncle Sah that is.

The big family

“Family is everything,” many of us like to glibly proclaim but it seems more like lip service than anything else, at least a lot of the time. We know now that all life shares a common ancestor, where our DNA ultimately came from. Our family literally includes the humpback whale, the bald eagle and the fruit fly. It's loud, boisterous, sometime bizarre and certainly diverse. Yes, family is everything.

The Human Genome Project was completed in 2003. We identified the approximately 20,000-25,000 genes in human DNA, the instruction manual for making a human. We also determined the sequence of the 3 billion chemical base pairs that make up human DNA. We have enough data now to study and analyze for the next 100 years. DNA in living cells, to the best of our knowledge, is universal and combined with the theory of evolution is a model of how life is, came to be and its origins.

Knowing what we know

Geneticists speak about “pseudo genes,” genes that once functioned in our ancestors but are no longer functioning. But of course, we haven't always been human. It appears in fact that we have not evolved that much because our evolution has been more about loss of gene function.

This is where environment has a great deal to do with who we are today. A million years ago one of our ancestors “discovered” fire and some 10,000 years ago began the Neolithic Age and the development of agriculture. Diets changed, food was cooked, cooperation and communication on a large scale became necessary and we consumed more starches.

Over a relatively long period of time we found we no longer needed such strong jaw muscles, which required a bony head that limited brain development. Our heads gradually became round, which helped increase brain size.

Both chimps and humans have the amylase gene for digesting starch but chimpanzees have two of these genes and humans have six. As farming culture developed this particular gene became more important. Interestingly, human populations that do not farm, such as the Australian aborigines, have fewer amylase genes.

Some 75 percent of our identified disease causing genes, such as Huntington, Parkinson and some types of cancers have been identified in fruit flies. As well, what is called the pax6 gene regulates eye development in flies, mice and ourselves. The fruit fly has turned out to be extremely important in analyzing certain conditions found in humans. Fruit flies respond like humans to alcohol consumption, from hyperactivity to passing out. They're used in studying insomnia and severe aggression, and altered serotonin levels in flies have resulted in a male-male sexual orientation in the mutants.

The Neanderthal, who died out some 25,000 years ago, is probably the last divergent branch of our evolutionary tree. Approximately 2.5 percent of our DNA outside of Africa comes from the Neanderthal. We likely met up somewhere in the Middle East for a brief encounter.

The FOXP2 gene, which is called the language gene, is identical in both humans and Neanderthal. It appears however that certain genes in cognitive development are different between humans and Neanderthal, possibly because Neanderthals and humans had to solve different types of problems, like anticipating prey for example or simply “life styles.”

The short and long of it

All life on this planet is intimately related. It goes way beyond “loving thy neighbor.” The “them” is us. Homo sapians, collectively, are not an especially lovable species and one could argue that the planet would be better served if we simply went away.

On the other hand, an evolutionary breakthrough could occur, a gene switched on or off and our behavior changed or modified. The extraordinary achievement of mapping the human genome (as well as other species) has the potential for amazing possibilities, both good … and bad. A good first step is understanding how large our real family is and our responsibility in protecting it. That may be the best hope for our survival.

For Americans in particular and global enlightenment in general

If human beings are basically tradition-bound, irrational creatures, how did science ever develop in the first place? The short answer is, “With difficulty.”

(Uncommon Sense: The Heretical Nature of Science, by Alan Cromer)

A state of bliss

Buffoonery has become a pervasive condition in America, as observed on an almost daily basis, especially among the political class. The latest example is a relatively obscure Republican congressman from Texas, Representative Lamar Smith. Mr. Smith, with no scientific expertise and apparently no understanding of the basic scientific process, happens to be the Chairman of the House Committee on Science, Space and Technology.

Representative Smith has drafted a bill that, while directed at The National Science Foundation, one of the premier scientific institutions in the world, wants to set in motion a process for all federal science agencies. His goal is to replace peer review and reduce the importance of scientific replication with some kind of “criteria” chosen by Congress, a criteria that seems to have less to do with science than it does with politics and what Mr. Lamar and some of his colleagues like or dislike.

The chairman of the committee wants to be certain that any grant given out by the NSF has “intellectual merit.” He claims to want to halt “frivolous” and “wasteful” research being funded and insure that any research that is funded be extremely important to “society at large.”

Now how could anyone be against good governance and saving taxpayer money? ( The proposed 2014 science budget is approximately 0.2 percent of the $3.77 trillion federal budget.) After all, U.S. Senator James Inhoff has made a career promoting climate change as a hoax. It's about greedy scientists wanting research grants, as Inhoff will tell anyone who will listen. For details on this dismal and ideally short-lived episode see “Additional Reading.”

The expanding universe

What we refer to as modern science began more than 300 years ago and it has met with resistance of one kind or another the same length of time. Yes, there have been some eureka moments but mostly knowledge was built on what went before. Scientists always owe a debt to those who came before them.

Over the same period of time the scientific method was developed and improved upon. It didn't matter if you didn't like the outcome of the experiment or that your familiar world view turned out to be wrong. The Earth really does go around the sun and it can be demonstrated by a lot of people. Our planet is more than 4 billion years old, and best of all it's not a closely held secret known to only a chosen few.

Scientific research, both public and private, must be robust and intellectually honest. It can be hypothesis driven (to answer a specific question) or discovery based (no specific hypothesis in mind). Above all, none of us--anywhere--can be complacent whenever the usual suspects attempt to turn science into something it's not. It is time to once again confront the usual buffoonery. Make it loud and persistent. It's in the self-interest of all of us.

Additional Reading:

U.S. Lawmaker Proposes NewCriteria for Choosing NSF Grants

A rebuttal to Lamar from theranking member of the House Committee

National Science FoundationMerit Review (The NSF process for reviewing a grant application)

The Scientific Method: AnOverview (An explanation of the scientific method for high school and junior high school students)

SOPA creator's latest billproposes stripping peer-review from science funding

2014 proposed science budget

Follow up: "When consequences are bad"

Chapter 2

The Reinhart-Rogoff analysis has set off a firestorm, at least among “insiders,” and that's a problem in and of itself. The real question for most of us who are not economists, statisticians or think tank specialists is will there be some positive outcome as a result of this uproar?

The only truthful response is that it's hard to say at this point in time. In America at least, most of us, rich and poor, have been uncomfortable talking about “class war.” It has however been the monster in the closet or the crazy aunt in the attic for most of our history, especially after the Civil War ended in 1865.

Paul Krugman in a recent NYT article (The 1 Percent's Solution) said that, “What, after all, do people want from economic policy? The answer, it turns out, is that it depends on which people you ask.”

There have been a flurry of articles about Reinhart-Rogoff. Jared Bernstein, a well known economist currently at the Center on Budget and Policy Priorities, in a recent article in Salon (How to prevent future Reinhart-Rogoff melt downs) said—without actually saying it—that economics is not real science. No it's not and never has been. For those interested in learning more about the Reinhart-Rogoff analysis and what it means from the arcane to the general see 'Additional Reading.'

What have we learned

This story, like so many others, is really about that we all have some responsibility for what happened. Of course we ought to develop a keener skepticism about what “experts” claim (far different from cynicism), demand better informed journalists and commentators, demand a more rigorous intellectual process in the field of economics, demand that public officials have a degree of integrity and knowledge and ultimately demand a citizenry (at least a significant portion) that is not so uninformed and disinterested as to be mere impediments to change. This story will continue (globally) for some time to come.

Additional Reading:

the numbers

Reinhart and Rogoff:Responding to Our Critics

Reinhart/Rogoff and Growthin a Time Before Debt

Comparing the Two Analyses

in general

There's no need for all thiseconomic sadomasochism

How much unemployment didReinhart and Rogoff's arithmetic mistake cause?

Rogoff and Reinhart should show some remorse and reconsider austerity

When consequences are bad

Knowledge is a public good and increases in value as the number of people possessing it increases.

(John Wilbanks, vice president of science at Creative Commons)

The issue

Let's call it the Reinhart-Rogoff brouhaha, which virtually no one knows about, well, almost no one knows about it, except some economists, public policy types and maybe some literate politicians. It turns out to be important however because it impacts probably the majority of Americans as well as a lot of non-Americans throughout the world.

Carmen Reinhart and Kenneth Rogoff are two well known Harvard economist that have exerted considerable influence on the economic policy of the U.S. and likely in Europe as well. Their influence has been on the side of economic austerity rather than economic stimulation, beloved by not just conservatives and assorted ideologues.

The Reinhart-Rogoff “law” (it's not) states that once a country's gross debt to GDP ratio crosses the threshold of 90 percent, economic growth slows. Debt therefore becomes terrifying, a monster to be avoided, a nightmarish scenario that will destroy civilization. Uh-huh.

(For a clear explanation of the Reinhart-Rogoff controversy see Paul Krugman's article in the NYT, 4/18/13, entitled The Excel Depression).

The science thing and the problem with Reinhart-Rogoff

What we call the modern scientific process had its beginning in the 17^th century. It gradually began to systematize knowledge about the natural or physical world and constructed the elements of the scientific process. It has generally worked remarkable well, in part because it's transparent and concerned with HOW things work.

If you take the spectrum of science today you might go from physics to chemistry to biology to medicine to the social sciences, no one area more or less valid than the other—in terms at getting at the “Truth”--but the degree of quantitative validation and specific proof is more demanding in physics, for example, than probably any other area, at least for the moment.

What seems to stand out as you learn the basics of the Reinhart-Rogoff study, which was first published in 2010, is how sloppy the original analysis actually was, in many ways making it easier for those individuals who wanted to to jump on the austerity bandwagon.

It turns out that data was missing, questionable statistical procedures were used and an important coding error was made. Correlations were suggested in the study but those are not the same thing as “cause.”Hypotheses were seemingly offered as facts, but the long and short of the study is that there was never a “90 percent threshold.”

No, economics by any stretch of the imagination can not be called “hard” science at the present time, but the subject could use a far more rigorous process in determining the validity of many of its key concepts, especially in light of its central role in public policy and the impact on individuals. Alan Greenspan, former head of the Federal Reserve Bank, said back in 2008 that, “We were wrong quite a good deal of the time.” Greenspan was a master of understatement.

In fairness, as Paul Krugman has pointed out, there were economists that were skeptical of the original study but it took a 28 year old graduate student from the University of Massachusetts more than two years later to drive a stake through the mystical dogma of the Reinhart-Rogoff study. Reinhart and Rogoff finally allowed researchers to look at their original spreadsheet and—the results couldn't be replicated, replication of course happens to be a basic early step in the scientific process.

Searching for a conclusion

The Reinhart-Rogoff study appears to be a fairly deceptive piece of work, which most likely has led to some unsound economic policies for the United States and some unwanted consequences overseas. Yet, it probably raises some larger questions as well.

If, as we Americans proclaim, at least officially, a democratic society of some kind requires a reasonably informed and engaged citizenry … well, which way are we going?

Second, beware of the “temple priests,” be they from the public or private domain, setting themselves up as the guardians and protectors of our knowledge. We can find them almost everywhere today, classifying documents of one kind or another, claiming patent protection for virtually everything and stifling open inquiry whenever possible—in the name of the public good of course. What will we ultimately decide to do? It requires some effort.

Additional Reading:

Does High Public DebtConsistently Stifle Economic Growth? A Critique of Reinhart andRogoff (Hendon, Ash, Pollin analysis of the Reinhart-Rogoff study, Univ. of Massachusetts, 2013)

The Conscience of a Liberal: Paul Krugman's blog   

A new perpetual motion machine

Laura Snyder, a science historian and professor of philosophy, has stated that the word “scientist” was used for the first time 180 years ago at a meeting of the British Association for the Advancement of Science, on June 24, 1833. Has it been only 180 years?

Prior to this time those who pursued “scientific” endeavors, mostly gifted amateurs, called themselves natural philosophers. All this gradually changed as deductive reasoning ( testing hypotheses and theories) became a key component of science, along with the creation of new scientific institutions, external funding for scientific projects and a growing belief that science ought to be for the public good.

Patenting of nature

Fast forward 180 years and we currently have a case before the U.S. Supreme Court that deals with the very structure of life itself. It's unlikely that the majority of Americans and most people on the planet for that matter have the slightest idea what is being debated and the potential outcome, regardless of the Court's ultimate decision.

In simple terms, the case before the Supreme Court is whether or not a company can patent human genes. This is a case that could effect everyone—because it involves DNA, the blueprint for life.

What constitutes a new gene? Will research be stifled and the flow of information impeded? How does a company recoup its investment, sometimes millions of dollars? Who will have access to affordable new tests and procedures as a result of any genetic breakthroughs? These are only a few of the questions that will have to be debated--publicly--and which go way beyond the U.S. Supreme Court.

The Joe Barton's rule

Joe Barton, a conservative Republican congressman from Texas and strong supporter of the fossil fuel industry, once apologized to BP (the company that caused the worst oil spill in U.S. history) because the White House demanded that the company pay millions of dollars for the clean up of the Gulf.

While the congressman claims that climate change does exist, he has consistently denied that there is any human connection to climate change. He cites the great flood in the Old Testament, before humankind burned hydrocarbons, as proof that the climate certainly changes, but humans have nothing to do with it.

Congressman Barton clearly has every right to his beliefs and he can certainly cite the Old Testament as “proof,” but it has nothing to do with modern science, and that is a big problem and not just for Americans.

Magical thinking

If you were to Goggle “perpetual motion machines” you would uncover a colorful history going back to at least the Middle Ages. Hope springs eternal. The pmm is a machine that continues to do work forever without acquiring energy from an external source. The problem is that it violates all the laws of known physics, like conservation of energy, thermodynamics and Newton's laws of motion. But people keep trying. It's the Joe Barton rule and that is a big problem.

The ecological economist Herman Daly has said that it's “politically impossible to stop growth,” while at the same time it's “biophysically impossible to continue it ad infinitum.” We may need another 180 years.

Planet of the mice

“Humans are here by the luck of the draw,” remarked the late paleontologist and evolutionary biologist, Stephen Jay Gould.

The escape

It only requires some imagination: In 2012 twenty so-called "super mice" escaped from an animal research lab in upstate New York. Eight of the youngest adults had human glial cells grafted into their brains as newborn mice. Scientists believe these cells play an important role for humans in both intellectual and cognitive processing capabilities.

Researchers demonstrated that the mice had "improved" cognitive capabilities, which included memory, learning and adaptive conditioning. The remaining twelve mice included 6 that had had their mysostatin gene shut down, resulting in increased muscle mass and strength. The other six had undergone therapy resulting in changes in slow-twitch (fatigue-resistant) and fast-twitch (bursts of power) muscles.

These mice could run about an hour longer than the 90 minutes a normal mouse can run before fatigue sets in. A house mouse is able to run approximately 900 meters or slightly more than half-a-mile, while these enhanced mice proved to be capable of running some 1,800 m, more than a mile. Along with their endurance, these particular mice were also resistant to weight gain because of an increase in fat-burning muscle. Is all of this science or pseudoscience?

The 20 escaped mice is fiction, but the particular experiments have in fact been done in research laboratories and reproduced, replicated and undergone peer review, all part of the scientific process.

The best of all possible worlds

Mid Missouri Public Radio recently had a piece on Kevin Wells, a scientist at the University of Missouri—Columbia. Wells has been studying genetics in animals for more than twenty years and he is well aware of the scientific possibilities, such as making animals resistant to swine flu, along with the potential concerns, such as the human health impact, animal welfare and yes, animals escaping.

It's quite likely we'll have a genetically engineered Atlantic salmon on the U.S. market fairly soon, breakthroughs for better treatment of human brain disorders not far off and possibly even “enhanced” Homo sapiens sooner than we think.

Some sort of genetic future has already arrived. What are we willing to do in terms of genetic engineering and what kind of public policy debate shall we engage in? If we have a scientifically illiterate society and a disengaged citizenry, are we capable of making rational choices and understand those that we've made?

But back to our 20 missing mice. The year is 2100, 87 years from now. A certain percentage of our super mice from 2012 survived and produced off springs. Might they have evolved faster than humans? Will they look far different from the average house mouse of today and how big could they get? Could technology out pace our ability as humans to understand what we have set in motion?

The Theory of Evolution does not say that life moves inexorably toward a higher level of complexity and maybe our mice will not, but it is about the “luck of the draw.”