Article: Humans responsible for demise of gigantic ancient mammals

Scientists claim their research settles a prolonged debate over whether mankind or climate change was the dominant cause of the demise of massive creatures in the time of the sabretooth tiger, the woolly mammoth, the woolly rhino and the giant armadillo. 

Humans arrive, and megafauna went extinct. The authors had no way of determining if the extinctions due to hunting, competition, or habitat change.

Examining different regions of the world across these scenarios, they found coincidences of human spread and species extinction which illustrate that man was the main agent causing the demise, with climate change exacerbating the number of extinctions. However, in certain regions of the world -- mainly in Asia -- they found patterns which patterns were broadly unaccounted for by either of these two drivers, and called for renewed focus on these neglected areas for further study.

Article: Grammar: Eventually the brain opts for the easy route

Languages are constantly evolving -- and grammar is no exception. The way in which the brain processes language triggers adjustments. If the brain has to exert itself too much to cope with difficult case constructions, it usually simplifies them over time, as linguists demonstrate in a study on languages all over the world. 

The grammar of languages keeps reorganizing itself. A prime example of this is the omission of case endings in the transition from Latin to Italian. 

Then how did language get complicated in the first place?

Article: Is the Science Ever Settled? Theories, Hypotheses, and What Science Really Does

Exploring what the theory of evolution really says gives us a good example of what science really does.

The article sticks pretty close to evolution, although it is applicable to thinking about the catastrophic anthropogenic global warming hypothesis, as well.

As a believing Christian, I accept that God created the heavens and the earth. However, I recognize that the theory evolution, as described in this article and elaborated over the last 160 years, is a powerful and elegant explanation for the diversity and genetic relatedness of life on earth. (Other than, "That is how God made it; deal with it," that is.)

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.

Feel-good article of the day

Article: Five Ways Liberals Ignore Science

Five major ways, and a host of minor ways, the left ignores science. And pushes an agenda behind that ignore-ance.

Article: Scientists Find Life Half a Mile Below Antarctic Ice

A half a mile below the surface of the West Antarctic Ice Sheet, in a lake that hasn’t been touched by sunshine or wind in millions of years, life goes on. A large US expedition called WISSARD, led by a professor at Montana State University, has unearthed a thriving ecosystem of micro-organisms after drilling through the thick ice to reach Subglacial Lake Whillans in January of 2013...

Many of the micro-organisms found are single-celled organisms, called Archaea, that survive by converting ammonium and methane into energy in a harsh environment similar to those found elsewhere in our solar system, such as on Jupiter’s moon Europa.

The Archaea ("ancient life") are very simple, very ancient bacteria-like organisms. Frequently they use unusual metabolic pathways as sources of energy.

Since this lake has not seen light for millions of years, this entire ecosystem cannot be dependent on light energy like most of earth's life.

Faces: pretty and intelligent

Article: You really CAN tell how intelligent a man is just by looking at him, scientists say (and the key is a long face and bigger distance between the eyes)

'The ability to accurately assess the intelligence of other persons finds its place in everyday social interaction and should have important evolutionary consequences,' the team wrote in the journal PLoS One.

If so, why be able to assess the intelligence of men, but not women? Over evolutionary time, have women been assessed on other values, instead? [See below]

The team used static facial photographs of 40 men and 40 women to test the relationship between measured IQ, perceived intelligence, and facial shape.

Both men and women were able to accurately evaluate the intelligence of men by viewing facial photographs, they discovered.

'These results suggest that a perceiver can accurately gauge the real intelligence of men, but not women, by viewing their faces in photographs; however, this estimation is possibly not based on facial shape,' they claim.

'Our study revealed no relation between intelligence and either attractiveness or face shape.

 Article:  In Harsh Conditions, Men Don't Want a Pretty Face

Big eyes and full lips may turn male heads in Japan, but in Nepal, men aren't as interested in pretty, girly faces.

Those are the findings of a new study of men's preferences for female faces in 28 nations. The results reveal that guys are drawn to feminine looks – large eyes, pillow lips and a soft jaw — to a greater extent in countries that are the healthiest.

The reason for this difference isn't clear, but scientists suspect that evolution may drive these attractions, at least subconsciously. Men in harsh conditions may have a better chance of fathering children who survive if they mate with a woman who can hold on to resources, said study researcher Urszula Marcinkowska

Science Links for 8/15/2014

Article: Huge asteroid that 'could end human life' defying gravity as it moves towards Earth, scientists say

It "defies gravity" by rotating on its axis so fast that its surface at its equator actually experiences "negative gravity."

Asteroids are a collection of dust and rubble. Normally, they are held together held together by gravity, but this one is rotating so fast that it is held together by van der Waal's force. [A weak force that is due to attraction between molecules. It is related to hydrogen bonding.]

Article: Who's your mummy? Egyptian mummification older than was thought

Researchers on Wednesday said a form of mummification was being carried out there more than six thousand years ago, much earlier than previously thought. They said embalming substances contained in funerary textiles from the oldest-known Egyptian cemeteries showed mummy-making from as early as about 4300 BC.

There is evidence of mummification involving remains from around 2600 BC of Queen Hetepheres, mother of Khufu, the pharaoh who commissioned the Great Pyramid at Giza outside Cairo. There also is evidence of linen that contained resin being used to wrap bodies around 2800 BC.

The researchers were amazed to find that the plant, animal and mineral components used in preparing the mummies at the cemeteries in Mostagedda in central Egypt were essentially the same embalming "recipe" used thousands of years later at the pinnacle of the ancient Egyptian civilization.

Article: Little penguins forage together: 40% of studied penguins synchronized underwater movements while foraging

Olympic synchronized swimming for penguins!

Little penguins are the smallest penguin species and they live exclusively in southern Australia, New Zealand, and the Chatham Islands, but spend most of their lives at sea in search of food. Not much is known about group foraging behavior in seabirds due to the difficulty in observing their remote feeding grounds.

The authors GPS devices to track the little penguins.

The authors found that ~ 70% of little penguins' foraging tracks were in association with other penguins, ~ 50% of individuals dove while associating with other penguins, and ~ 40% exhibited synchronous diving. These behaviors suggest little penguins forage in groups, may synchronize their underwater movements, and potentially cooperate to concentrate their small-schooling prey.

Article: Ebola outbreak: the vaccine and 'secret serum' explained

Vaccines exist, but have not been tested on humans. They seem to give protection to monkeys. Because Ebola outbreaks are usually localized and limited. Vaccination will never be wide-spread (like polio or smallpox), and mostly given to health workers and the like.

This drug [the "secret serum'"] gives you antibodies directly, rather than waiting two to three weeks after vaccination for the antibodies to work. It could be used for treatment whereas a vaccine is more likely to be used for prevention.

Article: Competition for ecological niches limits evolution of new species

The article is worth skimming just for pictures of the birds.

Most new species are thought to arise in a three step process: First, a species expands its range. Then a barrier, such as a geographic event, separates the species into distinct populations. Last, development of the inability to interbreed -- reproductive isolation -- finalizes the speciation process. As this cycle repeats, it gives rise to a vast diversity of plant and animal species. 

In this study, Professor Price, Dr Mohan and their colleagues used several approaches to examine how geographic differences affect speciation by testing the niche-filling model: first, they asked whether the geography of the eastern Himalayas provided a greater number and diversity of niches that songbirds could occupy and adapt to. Second, they examined whether the rate of oscine speciation changed over time. Third, they investigated the diversity and abundance of resources available in different ecological niches.

These findings suggest that speciation and geography are intimately connected in the evolutionary history of the Himalayan songbird assemblage: initially, numerous morphological differences in feeding method and body size appear early in their evolutionary history, whereas only later did the fledgling species invade and adapt to available ecological niches at different elevations. Since available niches were filling up as new species moved in, younger and younger songbird species were usually competing for smaller and smaller niches. These findings are all consistent with the niche-filling model.

13 Scientific Terms You Might Be Using Wrong

Article: 13 Scientific Terms You Might Be Using Wrong

Good article.

Meteor vs asteroid, theory, fossil, etc.

I do have one objection: the "birds are really dinosaurs" meme. No, they are not. It is cool to be able to say that birds are descended from dinosaurs. It has the "shiver" of being amazingly counter-intuitive.

On the other hand, it is like saying humans are really reptiles or amphibians or segmented worms or bacteria because, in theory, humans are descended from extinct organisms that were reptiles or amphibians or segmented worms or bacteria. We aren't. They aren't. Case closed.

Besides which, this has nothing to do with the rest of the article. It is like the author had a cool fact that he needed to say. 

Charles Darwin's Beagle library

Article:  Charles Darwin's Beagle library

Researchers, working over a 30 year period, have reconstructed the library Charles Darwin had access to on his voyage. They have also made the library available on-line, roughly 400 books.

Most of the books were actually the property of the ship's captain.

Most were nonfiction: books about previous sea voyages, natural history books, encyclopedias.

Also included were a KJV Bible and Milton's Paradise Lost (a personal favorite of Darwin's). Darwin also had copies of the New Testament in Greek and German to help him keep fluent in those languages.

Oddly, Thomas Malthus's book, An Essay on the Principle of Population, was not included. This book was foundational for Darwin's theory of evolution by natural selection.

Four articles about genes

Article: Genetic link to autism found, known as CHD8 mutation

The mutation is found in 15 of 6,176 children with autism spectrum disorder. Additionally, there are some physical (facial) abnormalities. Obviously, this is a very minor cause of autism spectrum disorder.

On the other hand, it may point to other mutations that may cause other variations in the disorder.

Article: Chimp intelligence 'runs in families,' environment less important

The role of genes in human intelligence or IQ has been studied for years, but Hopkins' study is among the first to address heritability in cognitive abilities in nonhuman primates. Studies have shown that human intelligence is inherited through genes, but social and environmental factors, such as formal education and socioeconomic status, also play a role and are somewhat confounded with genetic factors. Chimpanzees, which are highly intelligent and genetically similar to humans, do not have these additional socio-cultural influences.

Take home thought: humans have more "plasticity" that chimpanzees. Our larger, and more highly developed, brains allow for more learned behavior, more "space" for nurture to influence development.

This is only reasonable. If you believe in evolution, and let your eyes sweep across the vast array of behaviors in the animal kingdom, you would realize that most behaviors among animals are "hard-wired." That is, animals do what they do because they are programmed by genetics to it.

Birds may learn the songs of their species, but only within tight boundaries. It is the difference between speaking or writing haiku and the vast expanse of actual human communication.

It is difference between birdsong and human songs and singing.

Article: How coffee protects against Parkinson's

A specific genetic variation discovered by researchers protects against Parkinson’s Disease – especially for those who drink a lot of coffee. Neurodegenerative diseases such as Parkinson's have a complicated background where both genetic factors and exposure to environmental factors are involved.

Coffee, is there anything it cannot do?

Article: Size of the human genome reduced to 19,000 genes

How nutrients are metabolised and how neurons communicate in the brain are just some of the messages coded by the 3 billion letters that make up the human genome.

"No one could have imagined a few years ago that such a small number of genes could make something so complex."

"The physiological and developmental differences between primates are likely to be caused by gene regulation rather than by differences in the basic functions of the proteins in question."

For the most part, each gene produces a protein. Most of the proteins are enzymes, catalysts involved in metabolism. The research found about 12,000 different proteins made by the human genome. The article did not say anything about the remaining 7000 genes; they may be the regulatory genes.

Article: Tibetans didn't get their genetic advantage from Homo sapiens

Article: Here’s Why Tibetans Can Live Comfortably At Crazy-High Altitudes

Researchers have discovered they [Tibetan] share a gene with our hominid cousin the Denisovans, who went extinct some 40,000 years ago...

Known as EPAS1, the gene allows Tibetans to absorb scarce oxygen without creating extra red blood cells—something the rest of us mortals must deal with at altitude...

Another example of microevolution. A mating, or several, transferred the gene to the human population of the Tibetan Plateau. The gene then spread through the population because it conferred an advantage to those bearing it.

Skin color, microevolution, and dehydration.

Article: In human evolution, changes in skin's barrier set northern Europeans apart

An example of microevolution.

It has already been hypothesized that the pale skin of Europeans is due to a natural selection-driven need for vitamin D. More UV-B can be absorbed by paler skin, producing more vitamin D synthesis.

The authors of this article add that paler skin in Europeans may also be due to mutations which reduce the ability of skin to conserve water and prevent dehydration. That is, Europeans have a reduced need to conserve water compared to their African ancestors.

Yet, there was an evolutionary tradeoff for these barrier-weakening [...] mutations, Elias said. Mutation bearers have a tendency for very dry skin, and are vulnerable to atopic dermatitis, asthma and food allergies. But these diseases have appeared only recently, and did not become a problem until humans began to live in densely populated urban environments, Elias said.

Evolution, crime and genes

Article: Criminal offending as part of an alternative reproductive strategy: Investigating evolutionary hypotheses using Swedish total population data 

We linked data from nationwide total population registers in Sweden to test if criminality is associated with reproductive success.

Convicted criminal offenders had more children than individuals never convicted of a criminal offense.

There is an idea I have run across from time to time in the popular literature that human evolution has stopped due to civilization. It is more commonly held among the progressivist left and the social sciences than biology. It is one of those "pernicious paradigms" that need regularly to be "falsified."

This article helps do so.

There are two "types" of evolution: microevolution and macroevolution. Macroevolution refers to the emergence of new species. This is the one rejected by creationists and Bible-believing Christians, mostly because of the time required for this to occur exceeds the 6,000 year timeline derived from the Bible for the history of the earth.

On the other hand, microevolution refers to shifts in the frequency of genes in a population. One characteristic or trait becomes more common (red-hair among residents of the British Isles over the last 4000 years, for example) as another becomes less common.

In other words, Sweden is seeing a shift in the frequencies of genes related to criminal behavior. And microevolution is occurring. In the USA, in the 1930's, the progressivist left advocated various eugenic programs including "sterilization of the unfit" to deal with this "problem." 
 
Add enough gene shifts, or microevolution, to a population in one place compared to a population in another place and the result is a new species. That is, macroevolution occurs.

One outstanding example of microevolution is the gene which allows human adults to digest milk. This gene is relatively rare in the human race as a whole. It was also uncommon among the early European peoples. After dairy farming originated in the Middle East, milk became more common as a food item.

There is a "natural selection" advantage to being able to use milk (and milk products) as food when it is available in large amounts. Dairy farmers with the gene migrated into Europe and displaced the original inhabitants, or bred with them. The gene became common among European peoples. The gene frequency in humans in Europe shifted and microevolution occurred.

Side note: "displaced." Europeans should remember that their ancestors "displaced" the original inhabitants of their countries just like the European colonists "displaced" Native Americans. Migration and out-competing natives are also examples of evolution in action.

See also: Article:  Archaeology: The milk revolution

I did not have the terminology for this while I was still in high school, but I realized that humans were undergoing microevolution. It seemed obvious to me civilization itself had to be a selection pressure. That is, civilization itself would have to cause shifts in gene frequency.

In my case, I am extremely near-sighted. I can do very little without corrective lenses. (I just called my ophthalmologist for my annual exam). I would not have survived in any kind of "primitive" society. My father passed these genes on to me and I knew that would pass them on to any children I might have. (Blessedly, neither of my daughters are nearly as near-sighted as I am). Multiply that by millions.

Civilization removed the selection pressure against nearsightedness, therefore it should increase the gene frequencies of the gene(s) responsible.

Multiply that by thousands of genes and there has been a lot of microevolution going on since humans left Africa (if you believe in macroevolution and the "old earth.") Or since the emergence of civilization(s).

One of the pernicious paradigms common on the left and in academia is that race is a cultural construct having no basis in biology. And that there is no such thing as human races. That is, mostly among non-biologists. Biologists know better, even when they may not say so due to social pressure.

How many races are there, what are (or were) their exact distributions, and how much difference between them is there? These are all matters of dispute. Biologically, there is no dispute that they exist. (That is not to say that some biologists may dispute that; it is just that the evidence is overwhelming that human races do exist.)

The problem, as "The Bell Curve" controversy showed, is that the open discusion of some measures of differences between races cause enormous offense.

Side note: if the scientific discussion of a possible genetic component to intelligence offends you, you need to step back and ask yourself why.

One cannot both approach this idea scientifically and be offended. Skepticism towards the idea, by the way, is not the same as taking offense. And denial of the possibility is not science.

And the winner of Wikipedia's influence list is … an 18th century botanist. Hear hear

Article: And the winner of Wikipedia's influence list is … an 18th century botanist. Hear hear

I really admire Linnaeus; definitely a "personal hero." Binomial nomenclature isn't even obvious today as the answer to the question, "How do we name organisms in such a way that all scientists find useful?" And yet it was a simple, elegant, and powerful solution to the complicated naming schemes that pre-existed his.

His second, world-class accomplish was to invent the classification scheme, grouping like species together (Kingdom, phylum (or division for plants), class, etc.) The system was used successfully for over a century. Then Darwin came along and Linnaeus's groupings of "like species" became Darwin's "related species." "Like species" were alike because they were all related; that is, descended from a common ancestor. It was a powerful confirmation of Darwin's ideas. (And, yes, I am a Christian.)

As side notes: Google's algorithm has to be suspect. It misses both Jesus and Mohammed. Either one rates higher for "top influence." The previous version of the algorithm had Hitler, Madonna, and Michael Jackson on top. So it needs some work to reflect reality. Unless, of course, you define reality as a "21st century encyclopedia."

It is especially ironic because the word, "algorithm," is derived from an Arabic word, al-khuwarizmi, after an Islamic mathematician.

And the article gets his name wrong, calling him Carl Linnaeus. His original name was Karl von Linne. He gave himself a latinized, binomial name (just like he gave to plants), Carolus Linnaeus. I am not certain why Wikipedia gives his name as "Carl".