Reaping the Whirlwind: protein function without stable structure


(Christy Hemphill) #583

Do you honestly expect people to be able to explain the details of entire disciplines, area of study that take people years to master, in a post on a discussion forum? At some point, you have to decide you are going to trust experts. It seems like you are completely unwilling to trust anyone else’s expertise, even when that expertise is validated by all the other experts in the field. If you can’t trust an assessment unless you have personally made it (and you are intent on making these assessments in relative ignorance, because you cannot possibly acquire the requisite knowledge and experience to master every field whose expertise you are doubting in what remains of your lifetime) then this whole exercise you are undertaking is a waste of time. Go golfing.


(Christy Hemphill) #584

Your responses to people explaining science to you are very similar to a flat earth guy I interacted with here a few weeks ago. I’m sure it makes you feel more secure in your preferred position to believe that everyone who disagrees with you holds their opposing views because of a lack of character or intellectual curiosity or both. But there is a time and a place for honest, intelligent people to declare an issue settled in their minds.

Not being “open” to alternative explanations to settled issues is not automatically a mental deficiency, it’s part of healthy learning and mental stability. Vaccines are safe. The earth is round. Climate change is real. Evolution is a demonstrable fact. Those are settled issues in my mind, and my unwillingness to open up debate and be “objective” about what “the other side” brings to the table is not a sign of intellectual weakness, it’s a sign that learning has already taken place and I’ve moved on to other open questions.

You are the one who showed up here in a state of ambivalence about what you know and with questions. Projecting your state of investigation on to everyone else and assuming that unless everyone else has the same open questions, they are closed-minded and crippled by cognitive bias is uncalled for.


(Raymond Isbell) #585

You seem to have forgotten that I told you I would be playing the devil’s advocate for the sake of debate. Now that we’re getting to essentials and details that matter where the evolution side seems to be wanting, the evolution side is crying foul?

I’m recognizing serious weakness in the evolution side and rather than getting a gracious recognition of those weakness and a way forward that seems hopeful, I’m told to quit and go play golf? Really?

It’s probably just as well. As you may have noticed, there are many scientists who are coming to recognize the same things that I and many other ID folks have learned. Evolution is simply a dog that won’t hunt. Some are slow to recognize it, and because of their deep personal investment in it, they won’t let go, no matter the facts. When finally forced to face their tenuous evidence and weak arguments, they retreat and say, “I believe what I believe, thank you very much.”

I think this well is dry, and it’s time to move on.

I wish all of you well.


(Chris Falter) #586

It is. It has also been verified in hundreds if not thousands of experiments. These experiments observe which segments of DNA get transcribed into RNA and which RNA segments get transcribed into corresponding proteins. (I might be using the wrong lingo here; biologists, please feel free to correct my terminology.) These experiments have provided the evidence that most of the human genome is non-coding.

Does that make sense to you, Raymond?

I have a junk shelf in my garage where I toss miscellany that I don’t really use, but might someday. So far I haven’t used any of it, but someday I might.

Junk DNA is the same. It is not in use at the moment, but every now and then some segment of it gets pressed into service.

The prediction of evolution is that disabling mutations can accumulate in a segment of DNA whose phenotype becomes unimportant. For example, many mammals though not all have accumulated crippling mutations in the gene that produces vitamin C. It was broken in humans, which is why sailors on long journeys need to eat citrus fruits. It was not broken in horses, who never get scurvy.

Does that make sense?

Some pseudo-genes have no function, such as the pseudo-GULO gene in humans. Others have reduced function or have been exapted into new functions such as gene or cellular process regulation.

Yes. Not only is it possible, but the non-functionality of many pseudo-genes has already been verified experimentally and published in peer-reviewed literature.

Bear in mind that some pseudo-genes have reduced functionality or new regulatory functionality. Real biology is complex. Biologists are not surprised.

I am surprised that you assert this, because you already acknowledged having read the article I posted that links a specific effect (larger spleen, helpful for underwater diving) and specific mutations. I also linked to several articles that link specific effects in cetaceans to mutations in specific genes.

In fact, biologists have established numerous other links between changed functionality (the effects) and specific mutations (the input). One example mentioned recently is the loss of vitamin C generation and mutations in the GULO gene. Other examples include lactase persistence linked to certain mutations in lactase regulatory genes (in humans) and improved apoB functionality linked to a specific set of mutations in polar bears.

So yes, through careful study biologists have established links from effects back to their genetic causes.

You’re asking good questions, Raymond. I hope you find these answers useful.

I do not understand why you are unable or unwilling to respond to this so far, Raymond. Are you planning to give it a go?

Yours,
Chris


(Chris Falter) #587

There is no such thing as a finished theory in science. Remember all the physics you learned at Stanford? Well, there is not a physicist on the planet who can tell you the first thing about what makes up 95% of the mass-energy in the universe. I am referring to dark matter (27%) and dark energy (68%).

You and I have a couple of choices in our attitudes to the theories of physics:

  1. Declare the whole lot of them appallingly unscientific and based on thinly disguised circular reasoning.
  2. Accept the usefulness of models like relativity and the standard model of particles that are consistent with large numbers of observations, even as physicists acknowledge that they have more work to do.

If you were to voice opinion #1 to physicists, you would not be surprised to hear them vigorously defend the discoveries they have made and the reliability of their theories. You would hear no small amount of criticism of your lack of knowledge about physics.

Or would you be surprised at such a reaction from physicists?

I wonder, because you have been expressing opinion #1 to biologists over and over and over in this forum. And yet you seem surprised that they defend the empirical foundation of their work.

I understand the frustrations of the biologists with you. Dozens if not hundreds of posts ago, I posted links to several different articles that discussed the links between specfic phenotypes (effects) and specific mutations (causes). Nevertheless, just a few posts ago you asserted that biologists have not been able to establish such links.

Yours,
Chris


(Jay Johnson) #588

My sister and brother-in-law, a retired USMC sergeant major, spent a decade at Parris Island in the '80s. A similar situation there. My niece died of metastatic breast cancer two years ago. Causal connection? No way to be certain … too many variables. However likely it may seem, no one can say with absolute, 100% certainty that her childhood exposure to toxic chemicals was the cause of her cancer.

The scientific medical literature on the causal link between toxic chemicals and cancer would be full of the same phrases. Your exposure to toxic chemicals was consistent with developing bladder cancer. This is how the scientific community in all the biological sciences – not just evolutionary biology – talks about things. They don’t make definitive statements because absolute certainty isn’t possible. So, when you point out the fact that they use language like “suggests,” and when your entire argument basically comes down to that singular fact, you’re not arguing against evolution, but against all of the sciences, including medicine. What if I said toxic chemicals could not have caused your or my niece’s cancer because the doctors and scientists can’t rule out every other possible cause? Would you agree with me? And what if you showed me the scientific literature pointing out the link between cancer and the specific carcinogen found in your drinking water, but I refused to believe it because the authors wrote: “The evidence suggests Carcinogen A causes bladder cancer.”

This is a very weak reed that you’re leaning upon.

Raymond, please think about what you’re saying. Dennis is describing how science actually works, and your retort is “that might be a good approach.” Ya think? Scientists have been using it for hundreds of years now with great success, and no one in any field of endeavor has designed an experiment that met your criteria of identifying and testing all possible scenarios. You realize that human beings are finite, right? We cannot even think of every possible interaction with the environment or with other systems, let alone identify and test them.

In sum, you’re setting the bar for what you count as “evidence” impossibly high. In fact, it’s so high that not a single branch of science would meet your test. You’re playing with loaded dice.

I don’t think you understand what the Intelligent Design movement is trying to accomplish, or what many of us here believe regarding God’s design and involvement with his creation.

ID is not an alternative explanation to evolution. “Designed” is not the opposite of “evolved.” Virtually every Christian here agrees with you that God designed and supervised his creation. The “design” aspect is not disputed. Many people have told that to you, but you still carry on the same way as if you never heard it. So, please listen and let this soak in …

The dispute between Intelligent Design and Evolutionary Creation is not about “design” per se, but about whether such design by an outside, “intelligent” agent can be scientifically demonstrated to have occurred. So far, ID theorists have been unsuccessful, and I personally believe they will never succeed in finding the scientific proof of design that they seek, because such proof would destroy faith, not encourage it. (As you, yourself, mentioned in several posts.)

It’s a fair question. I believe option 1, including the fact that God planned and designed this world. However, I also believe that the Lord’s thoughts are higher than ours, so trying to “reverse engineer” his design according to human thinking and methods of design is a fruitless exercise. With Pascal, I would argue that God has intentionally created our world to be ambiguous. The evidence is and always will be finely balanced, so that humanity, by the exercise of reason alone, can neither prove nor disprove God, but must approach him in faith. Here is how Pascal put it:

If the world existed to instruct man of God, His divinity would shine through every part in it in an indisputable manner; but as it exists only by Jesus Christ, and for Jesus Christ, and to teach men both their corruption and their redemption, all displays the proofs of these two truths. All appearance indicates neither a total exclusion nor a manifest presence of divinity, but the presence of a God who hides Himself. Everything bears this character… He must not see nothing at all, nor must he see sufficient for him to believe he possesses it; but he must see enough to know that he has lost it. For to know of his loss, he must see and not see; and that is exactly the state in which he naturally is.

If the atheist says, “Blue,” do you feel compelled to say, “Red,” even if you also see blue? Denying obvious facts about our world, such as evolution and the age of the earth, isn’t a winning strategy for evangelism. Have you seen the exodus among the younger generation?


(Peter Wolfe) #589

Well for me, the reason I see merit is that it seems to agree with the observed facts, i.e. I think evolution is sound science. To me, ignoring what one observes because it does not fit ones worldview is foolish and misguided. Have you considered the option that both God and Evolution can be true? That is why Biologos exists as I understand it.