The Amazing Reality of Genetic Life

The amazing, incredible reality of genetic life...

If I got to live, again, and was born with scientific ability, it would be difficult
for me to choose between the fields of astrophysics/astronomy
versus genetics/biology!

Genetics is a fascinating field of endeavor which has greatly altered how thinkers view Life and reality.

Consider this measured reflection from a science website:

"One of the surprises that came out of the Human Genome Project was how few genes (protein coding stretches of DNA) humans
have — around 23,000,
not that different compared to the fruit fly with 14,000,
and quite a bit less than rice, with 51,000."

Wow!
So we human beings, homo sapiens, are situated between
a fruit fly
and a grain of rice!
We have more genes than a fruit fly, but less than a grain of rice!

Sounds hilariously bizarre, like some sort of slapstick movie comedy.

What sense does all of this make?

Read on:
"Traditionally the metaphor for genes was something more akin
to a blueprint, — the “standard dogma” of Francis Crick: each gene codes for
one mRNA which codes for one protein — but now we realize that many are better viewed as switches or volume knobs.

Moreover, one gene can have multiple effects. Complexity arises not so much from
the genes themselves as from the connections between them.

These network properties are currently an enormously rich topic of research. For example, the way the network is connected can dramatically affect the interplay between robustness to mutation and evolvability (the ability of a system to generate heritable phenotypic novelty).

The same gene often turns out to be used throughout the animal kingdom:
you can take the pax-6 gene that controls eye development from a human and put
it into the part of a fly that controls wings formation and the fly will make a (malformed) eye on its wing.

The same gene that controls the formation of human arms also controls the formation
of wings on birds, fins on fish, and legs on centipedes!

Modifying the way these genes are “wired together” can lead to massive changes
in an organism.

The burgeoning new field of evodevo (evolutionary developmental biology) studies how evolution exploits these “toolbox genes”
to help generate the endless forms most beautiful we see around us.

Much remains to be understood, but adjectives
like remarkable, elegant, and awe-inspiring are apt.
Clay or Lego blocks?

In a fascinating book proposing a “theory of facilitated variation” biologists Marc Kirschner and John Gehrard point out that while
the Modern Synthesis implicitly used the metaphor of clay -- evolution could produce variation in almost any direction,
but in very tiny steps--
modern biology would be better served by the metaphor of Lego blocks:
reusable connectable units are more constrained in what they can do, but you can generate useful new variation in much larger steps.

Selfish genes, or control on many levels? The field of systems biology is challenging
the reductionist bottom-up primacy that has dominated biological explanation over the last few decades.

In a beautiful book, The Music of Life: Biology beyond the Genome (OUP 2006),
Denis Noble, a remarkable polymath and one of the fathers of systems biology, takes the gene-centric view of his Oxford colleague Richard Dawkins to task.

He asserts that we must look beyond the “selfish gene."

A better metaphor for understanding life is music, “a symphonic interplay between genes, cells, organs, body, and environment."
from the BioLogos Website

And this:
On the reality of evolution--
"One way to view the dogmatic nature of neo-darwinism as it is often presented in public is to see it as a reaction to the dogmatism of the creationists. The ‘uncertain’ (in the sense of lacking reason) faith in creationism is replaced by the ‘certainties’ of science.

But there is a conflation here of very different degrees of certainty in science. There can’t be much doubt about the fact that life on earth has evolved.

There is much less certainty about the mechanisms. Unlike Darwinism (Darwin knew nothing of mechanisms, genes were not known), neo-darwinism proposes the exclusion of many mechanisms that have in fact now been found to occur in nature.

Adopting the ‘certainty’ of evolution to clothe the ‘uncertainty’ of particular theories about mechanisms has been the cause of many problems in public debate on evolution.

It is perfectly possible to defend the virtual certainty that life has evolved while debating in the usual argumentative scientific way the uncertainties surrounding the question of mechanisms.

The truth is that amongst the many mechanisms now known we know very little about which were prevalent in evolution. The answer is likely to be that different mechanisms were dominant at different stages.

Evolution itself evolves."

from http://www.musicoflife.website/Answers-dogmatism.html

By biologist and evolutionist Denis Noble
from Wikipedia: "Denis Noble is a British biologist who held the Burdon Sanderson Chair of Cardiovascular Physiology at the University of Oxford from 1984 to 2004... He is one of the pioneers of Systems Biology and developed the first viable mathematical model of the working heart in 1960."

How amazing, incredible, and wonderful is Life and Reality!

In the Light,

Daniel Wilcox

Part #2: What Is Clarity of the Mind?

Continuing with the series, Purity of Mind and Heart:

#1: Use reason to clarify your worldview, when making major decisions, and in opposing what is false, wrong, and destructive.
Steer clear of informal and logical fallacies.

#2 Keep in mind that sometimes the term fallacy can even be used as a fallacy! For example, it has often happened in “appeal to authority.” An individual states 98% of plumbers in the U.S. think that such and such pipe is more reliable than…Or most philosophers think that…
And a person who disagrees says, “Oh, that’s just an appeal to authority—Fallacy!"

Nope. Showing that most authorities in their field support a view--the consensus--isn’t a fallacy, that’s evidence.

The fallacy, “appeal to authority” is when you argue most ministers, or most people in the U.S., believe that evolution is false. That is an error in authority because whether or not evolution is true or false is a subject for biologists to study and present evidence for one way or the other (97% of scientists say evolution is a fact).

Whether or not not most ministers, or most of the public, oppose evolution as false is not significant because they aren't scientists!

#3 Though carefully thought out reasoning is the watch-word, It’s okay, (even sometimes needed or necessary), to make intuitive jumps. Scientists and other thinkers often use intuition including famous ones such as Albert Einstein. Remember his comment about how imagination is more important than knowledge.

When making intuitive leaps, however, make sure it’s not near a cliff;-).

If you’ve been studying a project or issue in depth and haven’t solved the problem, then taking a break, even sleeping on it may help. One scientist actually made an important discovery in a dream.

However, if you are about to try out a new parachute, launch a rocket, get married, or change worldviews, it behooves you to double check your sudden intuitive insight with some careful thinking and evidence.

#4 When thinking through an ethical problem, be careful about semantic confusion, simplistic terms, and confirmation bias. Take a look at Peanuts:

And consider another example of confirmation bias, semantic confusion, and simplistic term-iteness:

"I'm pro-life! Strongly against abortion. We stand with America and our troops. Remember what our Christian leader said, God's gift to America
is the atom bomb."

Huh?



In the Light of Reason,

Daniel Wilcox

Plugging the Spiritual Sieve

Growing up in fundamentalism and evangelicalism of the Christian religion, we were continually warned about the “slippery slope of doubt and liberalism.”

My subsequent trials and steep learning curve of a university education at the University of Nebraska and Cal State Long Beach, and the many 'travailed'-roads of a spiritual journey
through lots of theological and scientific tomes and evangelicalism’s too many ‘easy-isms’—all that, has brought me too close to the dangerous cliff of a faith'd demise.

Which shows the question of the truth of that fundamental “truism” is both yes and no.

Slip and slide...

However, this short blog reflection is based not so much in the slippery slope metaphor,

but more in other striking images,
that of the “spiritual sieve” of Christianity--

How so much of religious faith is drizzling down through millions of small holes.




Or that of a wide funnel
and the eventual swirling down
at a hectic rush of all that used to provide
security and hope.





Or it's like an individual who runs around in his upward-bound basket of faith,
trying to patch the balloon above to keep the helium of his beliefs from leaking out
all the puncture wounds caused by secular learning.

Or like the boy in Holland who stuck his finger in a hole in the dike to keep out the flood of the sea.

But here in the bulwark of Christianity, tragically, there are thousands of holes to be plugged in order to keep the flood waters of fact and rogue waves of speculation--yes, the ocean of doubt, evil, and nothingness from drowning everyone.

And every thinking believer needs to run around constantly sticking his faith fingers in those endless holes, trying to stop dark gushing seawater from washing in and drowning us all.

A few of the Jagged Holes of the "Unholy" from the perspective of my childhood--

Evolution:
We were never "young earth creationists" in our family. My dad was a history major in college, and eventually earned 3 degrees. He considered Neanderthal and other ancient primates related to homo sapiens to be real, not the nefarious lies of atheistic scientists. So we accepted some form
theistic evolution.

But we strongly opposed natural selection. When I grew up, I constantly fought against Darwin's ‘unholy’ inundation; this ‘evilution.’

We Christians learned over and over again that Atheists held to this false ‘theory’ because of their sinful ways, that anyone could see there was no factual basis for Darwin’s concept, and it contradicted Genesis and the New Testament.

But in my first science class--Geology at the University of Nebraska, I quickly discovered, the whole issue was much more complicated and the evidence for secular science very overwhelming.

And I was totally turned off by the lame arguments that creationists used against evolution and for a world-wide Flood. After I completed my term paper on the latter, I was never the same, indeed, had moved into a modern scientific outlook.

Then came classes in anthropology, books on biology and many discussions. After years of intense struggle and a constant study of religion and science, I finally bowed the knee to objective fact, to the overwhelming evidence of geology, biology, chemistry, and physics.

So much for religious dogma, Christian illusion.

I did so finally because I could no longer deny hard evidence. I wanted to find out the real truth, did think that all truth is God's evidence. I no longer wanted to hang onto the security of questionable religious doctrine.

But believe me, I came kicking and screaming (to reverse a phrase from C. S. Lewis) into an acceptance of modern Darwinian evolutionary theory with its emphasis on "survival of the fittest" and random mutations.

It's very hard for religious humans to give up, essentially, their whole understanding of the nature of life.

But, especially, after Francis Collins (a Christian evolutionist) and other scientists finished the Human Genome Project which again showed the high probability of common descent of humankind from primates, I realized I had lived in a delusion based on faulty, and at times, ludicrous arguments.

Better late than never, though I wish I could have gotten there years earlier.

Many anti-evolution Christian books were so weakly reasoned and so missing in substantive factual evidence. Some even put forth ridiculous views such as claiming God had hidden dinosaur bones in the earth to mislead modern scientists! At least my parents had never believed in that!

If I hadn't seen horrific ethics displayed by non-religious individuals at university, I probably would have changed sooner (but that's another article to be explained later).

Inerrancy:
It was at 11 years of age that I first encountered severe doubts about part of the Bible. The story of Elisha and the 3 Bears;-) Well, it was only 2, and it wasn't cute or funny--because on order of God, the bears mauled 42 kids (2 Kings 2:23-25)!

We were taught this story in Sunday School. I remember becoming very upset, and telling our teacher and the other elementary students so.

How cruel and unjust! All that the boys had done was only make fun of Elisha's bald head.

And the fact that the Bible repeatedly defended and condoned slavery also troubled my mind as I entered the teen years.

Still, I remember saying (when I was about 13 or 14), I would quit believing in the Bible if one comma was missing from the text. But then I discovered to my chagrin that punctuation was only inserted into Scripture in the late Middle Ages.

Later textural study opened huge wide holes in my spirit and mind.

And I learned scriptural transmission, literary interpretation, history, etc. until my balloon of faith in the Bible became one droopy stretch of plastic in a pig sty of natural slime.

In so many portions, there are horrific immoral, unethical, unjust stories like in Judges, Joshua, Samuel and Kings.

Theological Determinism:
Denial of the Good News for most humans by Augustinian-Reformed theology. Original Sin, Evil Infants, Predestination, Hell...

The first time I encountered a Calvinist was at a high school Bible study when the adult leader claimed that sometimes God would order us to commit immoral actions! And he told me personally that I should be willing to do what is immoral for God. Whew!

Then there was a famous Bible leader's almost obscene claim. That happened, when as a young adult, my friend and I visited a Presbyterian church.

The leader lectured the assembly that “every murder and every rape are planned by God” and that God only wills/predestines for a limited number of humans to be saved.

I became extremely upset and utterly confused! That was the first death knell for me of secure, simple Christian faith and the beginning of a death battle that has lasted through many years. I’ve survived, but at times I actually no longer wanted to live.

Obviously my faith changed drastically as I studied Christian history and learned that most Christians believed in determinism and that God had created most humans to be foreordained to eternal damnation for his own glory!

And that the Good News I had heard and loved and admired as a kid was a heretical aberration of orthodox Christianity!

When I read a large volume on the creeds of the Christian religions, I was horrified by their immoral ethics, and totally skeptical of their theological abstractions.

What did any of these complex, convoluted, despairing statements have to do with the Good News?





But after having already checked out Hinduism, Buddhism, and various forms of Atheism, and found them worse, I stayed with a form of liberal Christianity associated with Anabaptism, Quakerism, and the Enlightenment.

And I still experientially had inner trust in Jesus like when I had met him as a young person, the night I “asked Jesus into my heart.” Back then we were taught God loves everyone and Christ died for everyone.

But not a day passes now but which I need to do battle against the despairing determinism which is being promoted by famous Christian leaders of “limited atonement, unconditional election," and other such ilk which inundates modern Christianity.

This horrific hole is as vast as a galaxy.

A cosmic sieve into the abyss...

More unholy holes next time...

But for now, the wholly:-) Good News…

Despite the countless punctures which have emptied Christian doctrine and theology,
my experience of Jesus,
my trust in God, the Ultimate Reality,
my faith in ethical truth
my hope in human rights, justice, equality, compassion, honesty, fidelity, and so forth
are alive and well.

It’s not the holes in human religious constructions which count, but the whole Truth.

Thanks to life struggles and extensive learning I've gained a deeper, more complex faith in God.

In the Light,

Daniel Wilcox