Monday, June 28, 2010

Why I Believe in Darwinism 1: Junk DNA

I've converted to Darwinism. I know this will be a disappointment to many long-time, loyal followers of the Bouncing Ball.  But, P@J and Agnostic Joe and others have worn me out. Better to cave. Succumb. Join the club. I feel smarter, already! Bright, even! Ha! I've cast off the shackles of religious restraint -- I can do what I want and there are no (eternal) consequences -- flapjacks, anyone!!!!

I feel better already!

What turned the tide? Junk DNA, my friends junk DNA.

Read all about it:

1972: 98% of our DNA is junk -- just as we would expect if our bodies (and ourselves) are nothing more than the product of uncreated natural chemical processes + dumb luck!

Darwin is proved correct and creationists are sucky-pants!

And boy, are we dumb -- 98% dumb, dumb, dumb.  I'm a Darwinist, and I'm full of dumb!

From Wiki:

"Junk DNA, a term that was introduced in 1972 by Susumu Ohno, was a provisional label for the portions of a genome sequence for which no discernible function had been identified."

In other words, the term was the result of our epistemological limitations -- what we did not know, not what we did know.  And it was used to great propaganda effect by Darwinists.

"According to a 1980 review in Nature by Leslie Orgel and Francis Crick, junk DNA has "little specificity and conveys little or no selective advantage to the organism".

1980 still going strong!

2010: "The term is currently, however, a somewhat outdated concept, being used mainly in popular science and in a colloquial way in scientific publications...

Outdated concept? Outdated by what?  By discoveries that a lot of what was dismissed under darwinian assumptions as junk isn't junk -- and it's getting less junky by the day.

And what effect did labelling this stuff as junk have?

"... , and may have slowed research into the biological functions of noncoding DNA."

And that's a shame.

If intelligent design were the reigning scientific theory, it would have served the science community just as well -- better, even. And scientists would have declared their theory once again vindicated by directed effort that had demonstrated that discernible functions had indeed been found for this DNA -- as expected by the theory.

Darwinism is both lens and blinder.

But, fellow darwinists, this by no means undermines our darwinism -- based as it is, like Darwin, more on a preferred materialistic worldview than actual reality and our interaction with actual reality via the powerful but finite tool of science.

And that's the way the newly minted darwinian Ball bounces.


P@J said...

I’m not sure what your argument is here. The fact that some people at some point in the past did not fully understand all the functionings DNA is some sort of evidence that evolution by natural selection is wrong? Again, in the early days of a new paradigm, we didn’t have all the answers immediately? Therefore, God did it?

In 1972, DNA was a pretty new idea. It was immediately recognized that some parts of DNA directly encode known proteins, and others didn’t. Of these (unfortunately termed “junk”) non-coding sequences, some have been found to perform very important regulating functions, some have been proven to not to have any function whatsoever, and some other, well, we just don’t know yet.

The Orgel & Krick paper in 1980 was actually really interesting (thanks for the tip), as it is essentially a response to Dawkins’ “Selfish Gene”. As you no doubt already know, this is the idea that we should not think about evolutionary pressures being placed on organisms, but on DNA, that the organism really only exists to replicate the DNA, and it is the DNA that is evolving. Essentially, this means that even parts of a genome that are of unknown value or utility (or indeed of no value or utility) may exert their own selection pressures, and be preserved. This is a powerful idea, and perhaps paved the way for the Lenski experiments (which, contrary to your previous statement, demonstrate the random nature of macro-evolutionary change). This is cool stuff. (aside: does DNA have dignity?)

Or, in your alternate universe, these subtle changes in our understanding of biochemistry are proof that we were wrong all along, and the theories of Bronze Age goat herders are a better explanation of the varieties of life on Earth.

Joe said...

Actually P@J from a scientific point of view we are better served to believe in Intelligent Design than we are to believe in Evolution. Time and time again science has made the mistake of believing that certain 'things' are just hold overs from previous evolutionary forms and therefore obsolete in its present form. Junk DNA is one, tonsils are another, as are adenoids, appendices etc etc etc. If you assume there was Intelligent Design involved you are more likely to look at the function as a part of the design and not as likely to do damage through ignorance.

Ignorance is deadly as witnessed by a fellow I grew up with. He is now doing veterinarian research but as a young lad he read that if you castrate a rooster it will mature faster. His dad had just bought 250 cockerels and my friend dutifully castrated them all. The next day he went out to see how the cockerels were doing and found every one of them dead. It seems that if you remove the testicles of a rooster it will survive. If you remove the kidneys of the rooster it will not survive. Tis better to understand the design than kill through ignorance.

RkBall said...

So, he castrated the roosters by removing their kidneys? Are you sure you got the story right?

Joe said...

I got the story right. He mistook the kidneys for the testicles since in birds the kidneys and testicles lie right beside each other inside the bird's body.

RkBall said...

"evolution by natural selection"

There are three components to neo-darwinism.

1. Common origin.
2. Random, (i.e., undirected, purposeless unintelligent) mutation.
3. Natural selection.

Concerning these.

1. There is lots of evidence that points in the direction of common origin. As a theist, I'm completely open to follow the evidence wherever it leads. I can sleep well at night under any three scenarios.

a) Common origin and incremental differentiations and improvements (with one exception).

b) Common origin, incremental differentiations and sudden, miraculous adaptations (of at least one species - us).

c) Direct creation of various species using the software principle of re-use.

3. Natural selection. This is not even worth arguing about. It basically says that the fit survive, and survival is the sole evidence of fitness.

What is interesting about it is that even this definitive characteristic of darwinism has shades of purpose and design to it. The phrase natural selection was chosen to contrast purposeful human selection with a type of "artificial" selection by nature. It is almost as if nature has a mind -- and this was, in fact, a common idea circulating in Darwin's day.

But, of course, mindless nature doesn't select anything. Right from the get-go Darwinism was appropriating the language of agency, purpose, and intelligence. And this has continued to the present day (while denying agency, purpose, and intelligence).

2. This is where the controversy lies. Not with evolution, not with natural selection (and, therefore, not with "evolution by natural selection", but with the mechanism.

If, instead of darwinian evolution, the ruling paradigm had been evolution by intelligently designed and/or directed natural processes, it would have received compelling confirmation with the discovery of DNA, embedded language, code, encoding, communication, engineering, etc.

It would have been "game over".

Plus, a lot of false leads could possibly have been avoided -- vestigial organs, junk DNA, etc.

So, a lot depends on one's predisposition.

P@J said...

Thanks Joe. Your idiot friend couldn’t tell a kidney from a testicle and killed 250 Chickens, therefore ID is a valid science? Please. We are tying to have a real conversation here.

The problem with ID is that it is not a testable hypothesis, nor does it make any satisfactory predictions that can be tested or found useful, therefore it is useless from a scientific point of view. Your argument from vestigial organs is another tired creationist canard that has been addressed thousands of times. And it has no relation whatsoever to non-coding DNA sequences. None. Nada. Two completely different things.

“If you assume there was Intelligent Design involved you are more likely to look at the function as a part of the design and not as likely to do damage through ignorance.”
This is a ridiculous statement. If one was to assume Intelligent Design, then one would assume that systems in nature are designed intelligently, and make decisions based on that. And you would be wrong many times. You would assume a nerve wrapped around the bottom of the aorta could not reasonably be the only route of information from the brain to the larynx. You would assume that a baby’s head and shoulder could always pass through the space allotted in the pelvis, and that there is not need for messy interventions … ah, you can look up your own examples… examples of very unintelligent “design” abound in nature.

When it comes down to your health, do you want a doctor to look at the bible and say “that oughtta work” or look in a medical text and say “this has always proven to work”?

RkBall said...

"When it comes down to your health, do you want a doctor...."

Glad you brought this up. All modern medicine is predicated on the idea that human beings consist of bodily parts that have purpose, function, proper and improper operation based on their design. All of these must be discarded under atheistic/darwinian assumptions.

There is no purpose or intended function to a darwinian heart -- it is just something that "just is". And one cannot say that the heart is operating properly or improperly -- because there is and cannot be -- any such thing. It's just molecules in motion -- and some results are better than others.

And cancer cells are not wrong, or bad, or a malfunction -- because there is no proper function to begin with -- they are just mindless nature operating in a different way, or, if you prefer, natural selection trying different things to see what happens.

Everyone's a believer in design, purpose and correct/incorrect functionality when they step into a doctor's office. Once again, atheists step into a world made comprehensible by theism and absurd by the very beliefs they so doggedly cling to.

P@J said...

Yet another deflection, away from the original point. Remember that? The point that changing understanding of non-coding DNA sequences “proved” evolution wrong? Oh… right, I raised points couldn’t counter so you are re-deflecting. The standard pseudo-science response when the facts are against them. Oh, well.

Let’s address this point, and see where you deflect to next.

For one so dogged by vague definitions earlier (see “Dignity”), you seemed to be doggedly attached to some now, seeing purpose in every process.

But your first sentence is wrong. Modern medicine is predicated on the idea that there are biochemical and physical processes behind every observed phenomenon. If a person blushes when embarrassed, that can be traced to the release of known chemicals from the endocrine system that trigger vaso-dilation. In an evolutionary sense, vasodilatation has many “purposes” (temperature and blood pressure regulation, hydration control, wound healing, etc), which provide a survival advantage, and were therefore selected for. Those born without beta-adrenoceptors would have a survival disadvantage, and be less likely to pass that on to offspring. The presence of these also lead to many disadvantages, including their role in enclampsia (which killed about 10% of women during childbirth… another example of bad design). By understanding the biochemical process, medicine was able to counter it (such that women in western hospitals simply do not die of enclampsia anymore). Little regard in this case would be given to the “purpose” or “design merits” of enclampsia. Instead, the biochemical process is understood and countered, human ingenuity making up for very, very bad design.

You are almost correct: cancer cells are not “bad”, nor are ther “good”, they just are. Of course, if they are in your body replacing healthy cells, then that bodes poorly for your continued existance. If continued existence is an interest of yours, you might want to take efforts to kill them off. Of course, if your goal in life is to get to heaven, then maybe killing them off is contrary to your expressed purpose. But but calling them “bad” is like calling a lightning bolt that burns your house down or a coconut that hits you on the head “bad”. It’s illogical anthropomophism of a physical process.

RkBall said...

"(temperature and blood pressure regulation, hydration control, wound healing, etc), which provide a survival advantage, and were therefore selected for."

1. Please stop using the language of purpose and intelligence (regulation, control). The process you believe in has neither. Use language appropriate to what you actually believe. Stop stealing from language that suits a theistic conception of reality but which is nonsensical in yours.

2. Stop with the" selected for" language, already. It's trivial, as I have argued. I can "select for" a new Mercedes if it shows up in my driveway -- the thing that has to be explained is how it got there in the first place so it could be selected.

And random, purposeless, undirected mutation simply does not get the job done. It's preposterous that an uncreated, process, with no aim in mind (as you hypothesize), would accidentally produce exquisite results such as consciousness, mind, intelligence, repair mechanisms, instructions, code, taste, sight, feeling, memory, etc. It defies belief.

3. Also, no selection actually takes place, so, once again, stop using the language of purpose and agency and use language associated with a care-nothing dumb process. The ocean does not "select" which pebbles to drag out to sea and which to leave on the beach -- neither does nature "select" anything in natural selection. It's misdirection -- you're suggesting nature has a mind and will and potency it simply does not have. It's dishonest.

Stop stealing from the theist's world. Use language appropriate to yours.

Every time you open your mouth, you affirm a theistic understanding of reality, and contradict your own.

P@J said...

Sorry, I cannot cede the entire English language to you. If you demand that "selection" can only happen by an intelligent hand, then you may be stuck in a rut even I can’t get you out of. Enjoy it there. Alternately, please give me a word to describe how a shoreface “selects” which stones will be deposited high on the beach, and which will be deposited below water line, because the simple result is that larger stones are deposited at the highest energy points in the wave swash, and the "system" of energy dispersion "induces" the saltation of rounded pebbles while more tabular pebbles of similar mass are deposited "selectively". Or how adiabatic winds "regulate" seasonal temperature fluctuations in Fjord valleys, or how the orientation of the Van Allen Belts are "controlled" by the intensity of the solar wind. Please use only approved non-design words to explain these system. Apparently I have to vet words with you before I use then, lest they be construed as already belonging to theists…

“it defies belief” --- indeed it does. That is where belief fails, and knowledge rules. You see, the processes you list can all be traced to simple biochemical actions, thermodynamics, electromagnetic effects, and redox chemistry. Your “argument from personal incredulity” is an established logical fallacy. If you educated yourself, you would rely less on belief, and would find facts are more reliable, and potentially make for stronger arguments.

RkBall said...

"simple biochemical actions"

Great. Glad to learn that they are simple. You da man that knows these things. If they're simple, you should be able to explain them to me.

Please explain, in simple terms:

1. Consciousness. How did it emerge, step-by-step? What is it? What is the relationship between my sense of "me", and biochemical actions? Do "I" actually exist, or am I an illusion caused by simple biochemical actions? Am "I" equal to my body?

2. Sense of dignity. Since this sense resides inside a person, it must reside "somewhere". Where is it? How many molecules does it take up, and how much does it weigh? More importantly, since evolution is a simple process, how did dignity emerge from non-dignity?

3. Life. Life is the product of simple biochemical processes. What are they? Have you reproduced them in your basement lab yet?

4. Free-will. Does it exist? If so, how did free-will agency emerge from simple mechanistic, cause-effect bound biochemical processes? What are the simple biochemical processes that result in free will?

5. Please describe the simple biochemical evolutionary process that resulted in vision -- not the eye, vision. Was the first light-sensitive cell the result of a copy error, a switch being turned on, or what?

6. How do we go from muons to morality, anyway?

You're still stuck in the 19th century. "Simple biological processes" fits Darwin's protoplasm blob. It doesn't fit the world of complexity found in the simplest life-form. It is mind-boggling complex, and the final results achieved are fantastic.

And to believe that the results achieved - brains, consciousness, agency, moral sense, circulation system, digestive system, etc. etc. "just happened" is a belief that takes far more obstinacy than reasonable faith in powerful, purposeful Agency.

But, some people just feel more comfortable seeing themselves as animals, no better than dirt.

RkBall said...

"Or how adiabatic winds "regulate" seasonal temperature fluctuations in Fjord valleys, or how the orientation of the Van Allen Belts are "controlled" by the intensity of the solar wind. Please use only approved non-design words to explain these system."

In these cases, you have an object acting on something else. E.g., The wind acting on something else. So these words are fine -- you have actual (natural) agency at work here.

This is not the case with darwinian evolution. There is no posited agency. There is just life "happening". Mutations happen. Some things survive, some things die.

There is no selection taking place. It is a phantom metaphor. There is no object acting on another to make it either live or die -- the thing either survives, or not -- that is why the language of agency and intelligence is inappropriate.

The reason I insist it be dropped in favor of scientifically accurate descriptions is this:

The language used in darwinism turns darwinism into a surrogate Creator-substitute, making choices, choosing this, rejecting that, refining this, etc. to make darwinian evolution seem like a reasonable surrogate for belief in an actual Creator. It's misdirection. It's bait-and-switch.

Use honest words. Unless you can posit an agent, ditch the language of selection, purpose, etc.

RkBall said...

"Apparently I have to vet words with you before I use then, lest they be construed as already belonging to theists…"

It's not that they belong to theists -- it's that they are appropriate in a theistic vision of reality, and inappropriate in the mindless, purposeless, directionless, pointless, indifferent universe you claim as reality.

RkBall said...

"That is where belief fails, and knowledge rules."

Darwinism is a belief; DNA information, encoding, communication is knowledge --

-- and we've barely scratched the surface. There's more we don't know than do know. There is a world, a universe, a cosmos of complexity to it -- and all this from a dumb-as-a-rock process biochemical. Pretty sad to go up against a mindless, brainless process and come out second!

RkBall said...

Your “argument from personal incredulity” is an established logical fallacy.

Actually my argument is from "sufficient reason", or "sufficient cause", and I stand by it.

I am very, very, settled and sure about my theistic beliefs. I wonder how truly settled you are in yours.

What's the next DNA discovery going to find? More "regulation"? Yet more embedded intelligence? A mutation algorithm (gasp!).

Would you at least agree that if a mutation algorithm was found inside the cell -- that the cell is programmed to mutate to seek and discover adaptive forms -- that that would mark the end of darwinism?

P@J said...

So, as I predicted, instead of addressing my query directly, you engage in another deflection, toward supposed algorithms embedded in DNA that we haven’t found yet. There isn’t enough ibuprofen in the world…

Your list is a compelling catalogue of logical errors (I can’t make life in my basement lab, therefore, it isn’t biochemical) and questions so elementary that anyone with a primary education in biology could answer in a paragraph. Of course, if I were to provide the answer, you would criticize me of using a word like “create”, or “design”, claiming some sort of semantic victory while ignoring the actual point made. So it is fools game. Not interested. The answers you seek can be found in many texts or on the net. You are not interested in seeking answers, so quit pretending.

By the way, “protoplasm” was a Huxley term, never used by Darwin. No-one outside of comic books and certain Christian theologies use it now. But that is semantics

And there you go again with the argument from personal incredulity: “It is mind-boggling complex, and the final results achieved are fantastic”. Here we agree, but you stop there and say, since you don’t understand, it must be non-understandable, therefore God did it. Thati s just intellectual laziness. To mis-quote Sagan: I prefer the wonder borne of understanding over the wonder of ignorance.

P@J said...

“In these cases, you have an object acting on something else. E.g., The wind acting on something else. So these words are fine -- you have actual (natural) agency at work here.”

Not sure how you differentiate. In the case of evolutionary biology, you have one molecule (DNA) acting on another (amino acids), a natural agency at work. Life “happens” in the same way wind “happens” and rain “happens”, complex thermodynamic and chemical interactions. I just don’t understand where you are drawing the line, and how you can draw such a solid line. At what point is the complexity too high to be “natural”? Crystal formation? Ion exchange on clay particles? The sorting of pebbles on a shoreface? The North Atlantic Oscillation? Gluconeogenesis?

What criteria do you use to differentiate? Whether you understand, or whether it can be explained to you in simple terms within 10 minutes

P@J said...

Evolution is not a “belief”, it is an observed phenomenon. Much like gravity, or the emission of photons from some materials when a current is applied. Natural selection is a model that explains the observed phenomenon, just as Universal Gravitation and the Photoelectric effect are models to explain the other two. Observations fit the model, no “belief” required. Please don’t introduce your theistic language into a scientific topic

RkBall said...

"Evolution is not a “belief”, it is an observed phenomenon." Evolution is an observed phenomenon. Darwinism is the metaphysical belief system that currently accompanies it.

Joe said...

"Evolution is not a “belief”, it is an observed phenomenon."

I do wish it would hurry up though. I've spent half my life waiting for my pet rock to evolve into a living being. So far its just a rock.

RkBall said...

We can observe micro evolution of species e.g., via intelligent selection by humans in breeding. This was the inspiration for Darwin's "natural selection".

Most of the science of evolution is backward-looking, and it's based on a) materialistic philosophy, b) materialistic methodology, and c) induction, i.e., inference to the best explanation.

As soon as you discover that DNA contains what amounts to embedded intelligence, it's really game-over for the dumb-as-a-rock version of evolution that is insisted upon by person holding doggedly to a) above.

Darwinism, the universal acid, is materialistic philosophy wrapped in the white lab coat of science.

P@J said...

“Darwinism is the metaphysical belief system that currently accompanies it.”

Darwinism is a very poorly defined term, which is why I avoid using it. You will have to provide your definition of it before I can opine on whether it constitutes a belief system. It is definitively not metaphysical. More importantly, it should not be confused with Darwinian Natural Selection, which is the robust model developed to explain evolution, test hypotheses, and predict outcomes related to biological evolution. Again, no belief required.

P@J said...

Huh? Selective breeding by humans was Darwin’s inspiration? Now you are just making things up. You really should read “On the Origin of Species”, it is a very well written book, easy to understand but profound in its insights. If you are going to dismiss something as rubbish, you should probably read it first.

If the “inspiration” of an idea as grand and insightful as Natural selection could be boiled down to a few things, I would suggest in Darwin’s case it would be Lyell’s principles (especially uniformitarianism), Malthus’s ideas on limited resources, the distribution of finches and other species on the Galapagos, and recognition of the fossil record for what it really was. Pepper that with a healthy dose of 19th Century Eurocentrist racism. But we aren’t all perfect. Turing was gay, but that doesn’t prevent Baptists from using computers.

P@J said...

nice deflection #6, however. Keep it up, you may never have to defend any of your points of you keep changing the discussion.

"... nothing intellectually compelling or challenging.. bald assertions coupled to superstition... woefully pathetic"