Reaping the Whirlwind: protein function without stable structure

(Stephen Matheson) #202

Well, that first goal is one you share with me and with thousands of cell biologists and evolutionary biologists. As a Christian I didn’t see “contradictions” between science and the Bible, but my faith was probably a lot different from yours. But that’s one thing that is really great about this forum–you can meet and dialogue with fellow Christians who are knowledgeable and who share your interest in exploring science in the context of faith. In case you haven’t noticed, I have knowledge (of both science and Christian faith) but I don’t believe.

(Laura) #203

Just to interject as one who grew up on the teaching of AIG and other, even more fringe YEC gurus, I don’t recall detecting any kind of “lack of confidence” or expressions of feeling “unqualified” to judge. In fact, the whole point of Answers in Genesis is to provide answers. They simply believe that Genesis (especially chapter 1) provides scientific data about the creation of the world and won’t accept any data that contradicts this assumption.

(Stephen Matheson) #204

@DennisVenema used the best metaphor to answer this question. I’ll try a different illustration, one from biology, then I’ll stop attempting to explain. First I will just reiterate that there is no doubt that deep understanding of cellular systems can definitely illuminate and motivate questions about origins (more proximally, questions about relatedness and recent common ancestry). It just can’t answer those questions by itself.

So. Dennis referred to languages, which evolve via descent with modification. It should be obvious that one need little detailed knowledge of the languages themselves to understand how they have evolved.

Now consider a question from developmental biology. Any question will do but let’s use the liver. Mammalian livers can regenerate after injury. (Brains, in general, cannot.) How does this happen? Specifically, from what cells in the body do the new liver cells come? There are a few candidates: stem cells of some kind from within the liver, or non-stem cells from within the liver, or stem cells from a related tissue. Or non-physical intervention by a deity or other supernaturally powered entity. The point is that we know that livers regenerate but we don’t know the source of the new cells.

The question is hard to answer, but the information we need is this: what are the lineages of the new cells? Which cell is the parent, and which cell is that cell’s parent, etc. That’s the answer to the question. Deep insight into the metabolic networks of the liver cells will not answer the question. In this case, it can’t even help answer the question, and is instead a red herring. Many of our questions about liver cells remain unanswered, but we know very well that these answers will not help us understand the origins of liver cells during regeneration. The same logic applies to any lineage of any cell anywhere. You can be completely ignorant of now neurons work and still devise experiments to try to determine where those neurons come from during development.

I hope that helps, and will end my involvement in this particular sub-conversation by noting (for the third time, I think) that there are certainly times when deep systematic insight does help point to questions about origins. But it can’t answer them, because by definition the question about origins is a question about lineage, and relationship, and history.

(Raymond Isbell) #205

Thanks for that input. This really can only be resolved by understanding the nature of faith (πιστεύω) which means to accept as true and trustworthy. Those who are part of AiG, ICR, and other YEC groups take scripture at face value and have many sound arguments for believing the earth to be young. I’ve read Genesis in English, Hebrew and Greek and I have to agree with them that that is what Genesis as well as the rest of the Bible teaches. I’ve read what others have said when trying to interpret Genesis as allowing for longer than 24 hr days, but don’t find them compelling. With my current understanding of science, I don’t see any reason to challenge the YEC position. I see the science behind YEC as sound. I haven’t carefully studies OEC arguments so that’s why I’m in this forum trying to see the reasoning and thinking behind them. I’ve been given some excellent reading sources to look at so that’s my next step is to roll up my sleeves and read them. There are plenty of well meaning folks in this group who seem willing to help me understand it so I look forward to learning more so that if my position maintains, I will be able to say I’ve taken a careful look at both sides. At the end, I’ll provide a summary assessment of what I’ve learned, which side I take, and why. i’ll look forward to constructive criticism.

(Laura) #206

Reading and learning is always a good idea. It’s also important to be able to differentiate between a scientific claim vs. a theological one. This is where I believe many YEC organizations go wrong is that they try to force theological claims to become scientific and in so doing they cherry pick which scientific evidence they will or won’t accept – which is disingenuous if not flat-out dishonest.

I respect those who are doing what they believe is the best they can to faithfully interpret scripture, but I think it’s fair to say that exactly none of us “take scripture at face value.” If we did, we’d believe in a geocentric solar system and would accept transubstantiation, among other things. Interpretation and context are always a factor. Blessings on your learning and seeking.

(Randy) #207

Dr Isbell, good attitude to read. However, I think it’s ok to take a lifetime to get through this–and I think God isn’t impatient, so we can be confident it’s ok to take your time. I myself am still evolving (pun intended) and am grateful for those who have helped me with insight along the way, as well. God bless.

Addendum: If you get a chance to take the free on line course from Dr Lamoureux, or read his information, it helped me a lot. He became convinced of old earth (under Packer, I tihnk) when at Regent College in British Columbia (where he got a PhD, and then eventually of evolution in accomplishing his PhD in biology. He now teaches a course on faith and science in Alberta.

Here’s a discussion on our discourse Lamoureux’s Evolutionary Creation

Wow, that’s great.

I would agree that that’s what the old writers thought it meant. I would agree with Lamoureux, though, that God was using current idioms and pictures to convey truth–He said that God made it by speaking it–not that Marduk killed his mother and stretched her body across as the firmament. It’s sort of like the idiom of saying in the Bible that the sun rises–it doesn’t, but who would understand if the writer wrote that the earth turns to the sun? And wouldn’t that be confusing and completely ruin the reception? Lamoureux’ course is excellent in explaining this. He’s a Pentecostal and a scientist. (I’m a nondenominational missionary kid who married a Baptist, but that’s another story).

(Raymond Isbell) #208

I should add that knowing the languages helps, but it’s not something that makes you the final authority. Where the languages are the most help is in reading the Journal literature where the scholars give rigor in their exegesis. At least in the Journal literature you get to see all the options for interpreting a passage along with their hermeneutical reasoning. There’s lots of eisegesis at that level as well, so in the end, the rule I follow is simple. No interpretation is allowed that is not coherent and consistent with the rest of scripture. Even that’s hard to do since what I see as coherent and consistent may not be to others. That’s one of the big reasons I’m happy with our relationship to the Lord being based on faith/trust. I don’t have to prove it. I just have to trust Him. When I get to heaven, I have an endless list of questions. I can visualize Him saying to me in an exasperated tone, “Enough already!” Go outside and play!

Thanks. I’ll check those out. By the way, I would recommend Logos Bible Software for Bible study. It has a huge resource stock. It’s expensive but worth it.

(Randy) #209

Terrific way to put this! :slight_smile: thanks. I appreciate your discussion.

I heard that logos is good. I think @Christy would know a lot about that–she is a Bible translator in Mexico. There has been a thread about the different types of software for that on Biologos–I can’t find it right off the bat. Thanks.

(Raymond Isbell) #210

That’s zeal going beyond the evidence. In my younger years I was guilty of it. Now that I’m a little older and wiser, I try to be on guard to minimize it when I speak/write.

(Raymond Isbell) #211

I realize my brain is stuck in the mire of “engineering speak,” but how does lineage answer the question? As I’ve thought about it, I’m trying to understand why this is not simply kicking the can down the road, i.e., the closest link to the liver cell is another cell whose lineage is unknown except that it comes from its closest link which also is just as unknown as the two which sprang from it. I’m struggling to see how this type of reasoning will lead us to an answer if the answer itself points to another unknown. Concluding that evolution works because it explains “how that system got to be how it is” from its lineage seems like textbook circular reasoning unless you can prove where the first link in that chain came from and show that it came about by a Neo-Darwinian Evolutionary (NDE) process. That, however, is the crux of the debate. Is NDE a legitimate process? You can’t prove NDE is true by assuming it to be true farther up the chain.

I did some reading at the Berkeley Website on Evolution and notice that it defines a speciation events and their various possible causes. Interesting, but their explanations are all hypotheses. None are proven. The paper “Molecular evolution tracks macro-evolution transitions in Cetacea,” uses fossils to argue for macro-evolution, and claims that evolution of cetaceans has emerged as a poster child for macro-evolution. The paper’s language affirms the fact that their conclusions are hypothetical. It says, “Phylogenetic hypotheses for extinct and extant taxa are well developed, and include molecular divergence times among extant species with integration of extensive fossil data.” What I’m hearing is that hypothesis are the basis for concluding that macro-evolution is occurring. If a hypothesis can’t be proven, then is shouldn’t be used to conclude evolution is true. To do so is begging the question, and we know that circular reasoning is fallacious. What I’m starting to sense is that there are so many hypothesis that all conclude macro-evolution is the explanation, that it must be true. Is there such a rule in logic that says if you provide enough assumed truths about a hypothesis that it must be true? Or is it a more subtle (but fallacious) argument?

This is why I push the engineering approach to the problem. You must show somewhere along the trail that one hypothesis is true and is proven from basic principals. SE can do that, but since we don’t have enough knowledge of Cell detail, we can’t prove the important hypothesis that are a must if macro-evolution is to be proven. Where am I going wrong?

(Randy) #212

Thanks for your very humble approach. There are many who can articulate this better than I, but one of the things that convinced me in undergrad was the evidence of scars of evolution–imperfections that demonstrated change. One was the mitochondrial nucleotides, which reminded one of bacteria and implied ancient symbiosis. More convincing were pseudogenes, such as the vitamin C ones which are inactivated in the apes and man.

(Christy Hemphill) #213

Are you sure about that? There are ways to prove hypotheses by looking at genes. You don’t actually have to observe millions of years of reproduction happening.

(Jay Johnson) #214

You’re conflating the meanings of “hypothesis” and “hypothetical.” They aren’t identical. What you should be hearing is that two separate branches of science have examined two different types of evidence and come to the same conclusion.

No, there are so many lines of evidence that all point to macro-evolution that it must be true. When all the witnesses in a trial tell the same story, the verdict shouldn’t be in much doubt. The logical rule in play here is: “Can’t see the forest for the trees.”

(Raymond Isbell) #215

Thanks for the input Randy. One of the challenges that any researchers faces is that his/her research strategy, if successful, must verify that their hypothesis is true to a very high level of confidence. Absence of function or as you put it, evolution imperfections seem like a weak strategy. When I wrote research proposals I had to show that the conclusions I anticipated using the method I was proposing were more than just being consistent with the hypothesis. I needed to argue that my experimental results will demonstrate the hypothesis to be correct, and that there are no other interpretations of the experimental data that might raise doubts in the minds of fair minded reviewers. In the case of NDE vs ID or YEC, results must show that neither ID nor YEC are viable interpretations of the research data. I don’t think any research results can rule out ID or YEC. In Biology, for example, current ID models can easily explain such things as Robustness, Flexibility, and Redundancy (RFR) as designed Fault Tolerance (FT). Another is the forward error detection and correction (FEC) functionality discovered in the cell. That’s highly abstract and difficult to even visualize, much less design. To think it is integrated into the Cell to support transcription, etc. by chance is challenging for me. Functionality like FT and FEC strongly suggests ID or YEC over NDE. How many co-functions (proteins mutated at the same time and in just the right way to ensure coordinated function) must be in place at the same time to make that kind of functionality work? As I remember doing FEC, there was a lot of calculation, storage of intermediate results, more calculation, and verification. That’s C4 functionality on steroids. Where and how is that accomplished in the Cell? It’s definitely occurring, but where? What are the evolutionary intermediate steps to getting there? Thus, back to my question about proofs vs hypotheses. I see NDE as a hypothesis, but it appears to be a hypothesis built on other hypotheses, all unproven. You guys clearly see something I don’t so I’m looking forward to understanding it.

(Raymond Isbell) #216

Not sure I see what you’re saying. All hypotheses are hypothetical by definition.

(Randy) #217

Thanks. Hm let’s try this–

if you see a house whose roof has fallen in, but the walls and part of the struts are still standing, is that a good evidence for previous existence of a house? In the same way, a partially destroyed gene for Vitamin C production that exists in other organisms but is deactivated by methylation, etc, and is present in apes, is good evidence for common descent. @DennisVenema makes a good presentation on this in his Biologos blog and other parts in his videos on YouTube ( you can see I don’t shy away from long videos–I posted some on Andy Stanley a while ago, too!)

This is just one line of evidence–the video has more, but astronomy and varves, ice caps have great evidence for earth’s age, genetics for mutations and massive change…it’s pretty neat how they all come together. Something that makes me what to echo the Psalmist in praising God for how great His works are (and you do, too, I am happy to see). Thanks.

(Raymond Isbell) #218

My point is that evidence cannot be called evidence in any scientific way unless they are shown to be true. What I’ve seen so far is that what you are calling evidence hasn’t really graduated to that level. A hypothesis remains hypothetical until it has been show to be true.

Here’s a thought experiment: Identify two versions of a specie, one with and one without a new capability that came from the NDE process. Your hypothesis is that a mutation caused this observable change. Assume it’s the smallest observable/detectable change for experimental purposes. (Otherwise you can do the experiment. Isn’t this what we call testable?) Now look down thru the various sub-systems in the organism that has the change and identify how each sub-system is different from its baseline counterpart. Next identify the groups of cells that are different in each sub-system. Continue till you’re down to a single cell and identify which genes/alleles have changed and identify the specific mutations and the proteins. This exercise, if it could be done, would establish the kind of proof that would turn a hypothesis into evidence. If you can’t identify all the coordinated actions and their inter-relationships by all the proteins and the systems they comprise and conclusively show they are jointly responsible for the observable change in the organism, can you really say that you’ve proven your hypothesis? Can you call an unproven hypothesis evidence?

(Raymond Isbell) #219

Thanks, I’ll watch and get back to you. (Not tonight!)

(Randy) #220

Thanks. No hurry; take your time. By the way, @Kathryn_Applegate on Biologos staff, suggested in her book on “Why I Changed My Mind About Evolution,” to always come back to our mutual praise of God from our study of science, especially in discussing with other Christians–I appreciate doing that with you.

(Dennis Venema) #221

The facts are what they are (unless one is going to argue that there is some sort of conspiracy going on to hide the truth).

Whales have four limbs as embryos but a developmental program unique to whales arrests and reverses hindlimb development after it is already underway.

Odontocete whales (i.e. toothed ones) have the genetic remnants of the same genes all mammals use for air-based olfaction.

Primates have genes within them that are in the same genomic contexts as other mammals; these genes are functional in those mammals and their functions are understood; those same sequences are in the same genomic location in primates (relative to the surrounding genes), but they have mutations that remove the function we see in other mammals, and many of the inactivating mutations are shared between primates down to the nucleotide.

These facts are easily verifiable by anyone with access to the primary scientific literature and publicly available genome databases.

The million-dollar question is this: why are these facts the way they are?