Friday, August 16, 2013

Tracing the Y Chromosome, Studying Fossil Proteins, Seeking Truth

I could have written about a newly-identified critter called an olinguito. Instead, I picked news about four-billion-year-old fossilized protein, and Y chromosomes.

That sort of thing, and olinguitos, fascinate me. Your experience may vary:
  1. About Life's Origins: New Evidence
  2. X, Y, and DNA


(image courtesy NASA/JPL-Caltech)

Seeking Truth

I like living in the real world: which is why I like science, and being Catholic.

Catholics aren't required to keep up with what scientists are learning about this wonder-filled universe. But it's an option.

Honestly seeking truth by studying the world can't disturb faith, "because the things of the world and the things of faith derive from the same God...." (Catechism of the Catholic Church, 159)

Growing up in America, I understand why some folks assume that thinking and being Christian don't mix. Some loudly-religious Americans seem dedicated to perpetuating the idea that 'ignorance is next to Godliness.'

My take on God and the universe is that God seems to think big: which is fine by me. Not that my opinion matters in this case.

Thinking: a Duty and a Responsibility

"...Continue your search without tiring and without ever despairing of the truth. Recall the words of one of your great friends, St. Augustine: 'Let us seek with the desire to find, and find with the desire to seek still more.' Happy are those who, while possessing the truth, search more earnestly for it in order to renew it, deepen it and transmit it to others. Happy also are those who, not having found it, are working toward it with a sincere heart. May they seek the light of tomorrow with the light of today until they reach the fullness of light.

"But do not forget that if thinking is something great, it is first a duty. Woe to him who voluntarily closes his eyes to the light. Thinking is also a responsibility, so woe to those who darken the spirit by the thousand tricks which degrade it, make it proud, deceive and deform it. What other basic principle is there for men of science except to think rightly?..."
("Address to men of thought and science," John Paul VI (December 8, 1965))
Science and the Catholic Church got along back when it was called natural philosophy, although individual Catholics didn't necessarily like the idea of studying creation. That didn't change as the centuries rolled by. I've posted about Copernicus, Galileo, and getting a grip before. (October 26, 2009)

About a thousand years back, trade between Europe and the rest of the world started heating up. Manuscripts traveled along with consumer goods, giving European scholars access to knowledge from around the world.

Getting reasonably accurate Latin translations of documents from India, China, and the 'golden age' of ancient Greece must have been a heady experience. Small wonder that some European academics thought highly of ancient philosophers like Aristotle.

Aristotle and New Ideas

I like the old Aristotelian cosmology. Those nesting spheres made a nice, tidy, easily-visualized universe. It's a pretty good match with what folks can see without telescopes, but observations didn't quite match what Aristotle thought should be there.

In the 1200s some folks said that Earth might not be the only world. Others didn't like the newfangled idea, and insisted that God couldn't have made more than one world: apparently because Aristotle said so.

That's when the Catholic Church stepped in. Ever since 1277 Catholics haven't been allowed to say that there can't be other worlds.

"...That I Might Know the Organization of the Universe...."

Quite a few applecarts got upset in the 1500s.

The Catholic Church's reforms came too late to stop a protest movement from becoming a tool for northern European princes. England's Henry VIII and other rulers set up independent state-sponsored churches, helping them take political and economic control from Italian city-states.

Natural philosophy was recognizably 'science.' Folks like Tycho Brahe added fuel to the Aristotle/evidence debate.

Some scientists followed the evidence and decided that Earth goes around the Sun. Others didn't like new ideas: which is nothing new.

I don't know if there's a connection, but around 1550, Wisdom was edited out of the Bible. The book includes these verses:
"Now God grant I speak suitably and value these endowments at their worth: For he is the guide of Wisdom and the director of the wise.

"For both we and our words are in his hand, as well as all prudence and knowledge of crafts.

"For he gave me sound knowledge of existing things, that I might know the organization of the universe and the force of its elements,

"The beginning and the end and the midpoint of times, the changes in the sun's course and the variations of the seasons."
(Wisdom 7:15-18)
Looks like it's okay to "know the organization of the universe and the force of its elements."

We've learned quite a lot about "the organization of the universe" in the two millennia since Wisdom was written.

Faced with new knowledge, we have quite a few options. My preference is accepting reality, even if it's not what I learned in my youth.
"...These discoveries invite us to even greater admiration for the greatness of the Creator, prompting us to give him thanks for all his works and for the understanding and wisdom he gives to scholars and researchers...."
(Catechism, 283)

1. About Life's Origins: New Evidence


(Rob Bayer, Shutterstock.com, via LiveScience, used w/o permission)
"Stromatolites, shown here in Shark Bay, Western Australia, may be among Earth's first living microorganisms that produced oxygen, around 3 billion years ago."
"4-Billion-Year-Old Fossil Proteins Resurrected"
Tia Ghose, LiveScience (August 8, 2013)

"Researchers have reconstructed the structure of 4-billion-year-old proteins.

"The primeval proteins, described today (Aug. 8) in the journal Structure, could reveal new insights about the origin of life, said study co-author José Manuel Sanchez Ruíz, a physical chemist at the University of Granada in Spain.

"Exactly how life emerged on Earth more than 3 billion years ago is a mystery. Some scientists believe that lightning struck the primordial soup in ammonia-rich oceans, producing the complex molecules that formed the precursors to life. Others believe that chemical reactions at deep-sea hydrothermal vents gave rise to cell membranes and simple cellular pumps. And still others believe that space rocks brought the raw ingredients for life - or perhaps even life itself - to Earth. [7 Theories on the Origin of Life]...."
Whatever organic stuff was around when the first living things appeared on Earth is mostly gone now. One of life's characteristics is that we eat organic stuff, changing it into something new: which in turn gets processed through other organisms.

After a few billion years, the only organic stuff left from life's beginnings is are fossils that not even Earth's microbes have found edible.

Maybe someday we'll find a planet where life is getting started, and compare what we learn to what's we've pieced together about life back home. Until or unless that happens, all paleobiologists have to work with is what's here on Earth.

Origins

What we know for sure about how life got started, is that we don't know. Not with much certainty. Not yet, anyway.

When scientists realized that other planets were like Earth, some said that life began by being carried to Earth from another planet. I've seen that idea, panspermia, offered as an explanation for how life began. That seems rather silly.

It's not that I think it's unlikely or impossible that a major impact blasted rock containing Martian organisms into space, where they eventually fell to Earth. Material gets transferred between planets like that routinely, and we've learned that some microorganisms could survive the trip.

Panspermia may explain how life got a foothold here on Earth. As an explanation for how life began, it simply moves the origin point: without offering an explanation for how the process happened.

How and Why

How life began, when critters started producing oxygen, and how human beings changed into the sort of critters we are today: science is a useful tool for learning what happened.

Why things happen is another matter. (Catechism, 284)

Both questions fascinate me: how things work, and why. I don't see a problem with seeking both sorts of truth.

A Universe Filled With Life - - -

I'm intrigued by the organic compounds we've been finding between stars. Carbon compounds, like potassium chloride, ammonia, and vinyl alcohol, are the chemical building blocks life uses; and they're spread throughout what we can see of this galaxy.

We're also discovering new planets weekly. It looks like there's no cosmic shortage of material for making life. Whether or not there's anything, or anyone, out there is another matter. (March 22, 2013; December 7, 2012; January 29, 2012)

Maybe there are billions of planets where life has found a home. If that's so, we can learn what's unique about the terrestrial variety, and what's common for all living creatures. We may even find a way to define exactly what life is.

- - - Or Not

On the other hand, maybe we're standing on the only world supporting life: for now. If that's so, there's no shortage of raw materials we can use for terraforming. Although reforming a planet into a place that can support life is beyond today's technology, equipment developed for asteroid mining might be scaled up: and that's another topic.

I think the real challenge will be deciding which planet to start with. (June 28, 2013); Apathetic Lemming of North (January 5, 2010))

Vinyl alcohol is toxic for humans, by the way, but some critters 'eat' it. ("Biochemistry of microbial polyvinyl alcohol degradation;" Kawai F, Hu X; Applied Microbiology and Biotechnology (2009))

2. X, Y, and DNA


(Sebastian Kaulitzki, Shutterstock, via LiveScience, used w/o permission)
"A pair of sex chromosomes."
"Genetic 'Adam' and 'Eve' Uncovered"
Tia Ghose, LiveScience (August 1, 2013)

"Almost every man alive can trace his origins to one man who lived about 135,000 years ago, new research suggests. And that ancient man likely shared the planet with the mother of all women.

"The findings, detailed today (Aug. 1) in the journal Science, come from the most complete analysis of the male sex chromosome, or the Y chromosome, to date. The results overturn earlier research, which suggested that men's most recent common ancestor lived just 50,000 to 60,000 years ago.

"Despite their overlap in time, ancient 'Adam' and ancient 'Eve' probably didn't even live near each other...."
If they "probably didn't even live near each other," how could these two people both be ancestors to so many of us?

It's pretty straightforward. What these researchers did was trace what European royalty generally used to decide who gets to be king: the male line, father to son. I sketched out the sort of 'family tree' this article describes: the blue squares show the father-son line, pink ones the mother-daughter heritage.



That's just 'for example,' of course. I'd be very surprised if geneticists manage to trace that sort of individual detail for humanity's last 135,000 years any time soon: if ever.

My diagram might be misleading, by the way: men have mitochondrial DNA, too. I just thought it would be symmetrical to show a mother-daughter lineage alongside the other one. The 'mitochondrial Eve' comes up next. Moving on.

DNA and Picture Puzzles

"...Researchers believe that modern humans left Africa between 60,000 and 200,000 years ago, and that the mother of all women likely emerged from East Africa. But beyond that, the details get fuzzy.

"The Y chromosome is passed down identically from father to son, so mutations, or point changes, in the male sex chromosome can trace the male line back to the father of all humans. By contrast, DNA from the mitochondria, the energy powerhouse of the cell, is carried inside the egg, so only women pass it on to their children. The DNA hidden inside mitochondria, therefore, can reveal the maternal lineage to an ancient Eve.

"But over time, the male chromosome gets bloated with duplicated, jumbled-up stretches of DNA, said study co-author Carlos Bustamante, a geneticist at Stanford University in California. As a result, piecing together fragments of DNA from gene sequencing was like trying to assemble a puzzle without the image on the box top, making thorough analysis difficult...."
(Tia Ghose, LiveScience)
I've noticed that the more we learn about humanity's story, the earlier things happened. In the last few years we've learned that folks have used kitchens for upwards of 800,000 years. Cooking fires go back a million years: at least:

Y Chromosome

"...Bustamante and his colleagues assembled a much bigger piece of the puzzle by sequencing the entire genome of the Y chromosome for 69 men from seven global populations, from African San Bushmen to the Yakut of Siberia.

"By assuming a mutation rate anchored to archaeological events (such as the migration of people across the Bering Strait), the team concluded that all males in their global sample shared a single male ancestor in Africa roughly 125,000 to 156,000 years ago.

"In addition, mitochondrial DNA from the men, as well as similar samples from 24 women, revealed that all women on the planet trace back to a mitochondrial Eve, who lived in Africa between 99,000 and 148,000 years ago - almost the same time period during which the Y-chromosome Adam lived...."
(Tia Ghose, LiveScience)
Adam? Eve?? 150,000 years back???

Journalists use catchy, memorable words and phrases. Making accounts interesting and fun to read is part of their job. I did the same sort of thing during my brief stint in journalism, which had nothing to do with semipalmated sandpipers, and that's yet another topic.

Using the names "Adam" and "Eve" is metaphorically appropriate for the earliest known man and woman in some lineage. But in this case it doesn't have much to do with what's in Genesis. I'll get back to that.

Deep Roots

"...A separate study in the same issue of the journal Science found that men shared a common ancestor between 180,000 and 200,000 years ago.

"And in a study detailed in March in the American Journal of Human Genetics, Hammer's group showed that several men in Africa have unique, divergent Y chromosomes that trace back to an even more ancient man who lived between 237,000 and 581,000 years ago...."
(Tia Ghose, LiveScience)
No, this does not show that Africans aren't quite human, or that the pale mutants in my recent ancestry are a 'race apart.'

It does show that have more to learn about humanity's early millennia. It's also more evidence that our family tree's roots are in Africa.

What caught my eye was the age of this particular branch: once again, 'stuff happened earlier.'

Living in the Real World

"...These primeval people aren't parallel to the biblical Adam and Eve. They weren't the first modern humans on the planet, but instead just the two out of thousands of people alive at the time with unbroken male or female lineages that continue on today...."
(Tia Ghose, LiveScience)
In this context, "modern human" doesn't mean someone who buys the latest in personal tech, or lives in a 'civilized' country. A "modern human" is someone who could, with a haircut, appropriate clothes, and maybe some language lessons, go unnoticed in a cosmopolitan city like New York or Rome.

Folks haven't looked like this until quite recently, and we're still changing. No surprises there: not for me, anyway.

Change happens. It's part of this creation, which doesn't make it any easier to deal with: at least for some folks. That "biblical Adam and Eve" link is to an article about the Creation Museum in Kentucky, where folks who desperately want Earth to be 6,000 years old can get their assumptions validated.

I wouldn't go to the Creation Museum myself. I had my fill of Bible-thumping zealots in my youth. Their malignant virtue helped me become a Catholic, and helps me sympathize with folks discussed in this "new analysis:"
"...a new analysis argues that for people already alienated by religious fundamentalism, the museum can be a painful reminder of discrimination and isolation...."
(Stephanie Pappas)
Folks who believe that the universe is 6,000 years old and that everyone who likes the 'wrong' sort of music goes to Hell may be sincere: but I am convinced that they are wrong. Someone with that sort of belief might assume that as a Catholic, I have been brainwashed into believing that God isn't limited to Ussher's chronology.

As I've said before, I prefer living in realty.

Related posts:

2 comments:

JohnL said...

Thanks Brian for a good article. I likewise have similar tastes in my foraging about life, humanity and what makes every thing tick. In an earlier life I was a chemist (applied) later did social sciences. I am currently reading a book by Stephen G Meyer called "Signature in the cell." Would be right up your alley. Cheers

Brian Gill said...

JohnL,

My pleasure. I'd have acknowledged your comment earlier, but had fallen behind this summer.

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What's That Doing in a Nice Catholic Blog?

From time to time, a service that I use will display links to - odd - services and retailers.

I block a few of the more obvious dubious advertisers.

For example: psychic anything, numerology, mediums, and related practices are on the no-no list for Catholics. It has to do with the Church's stand on divination. I try to block those ads.

Sometime regrettable advertisements get through, anyway.

Bottom line? What that service displays reflects the local culture's norms, - not Catholic teaching.