Reaping the Whirlwind: protein function without stable structure


(Mervin Bitikofer) #142

First of all - Thank you, Scott, for taking the time to view that and leave those comments here - “waste of your time” that you deemed it to be. Since you are the one that took that initiative and effort to do that, it is hardly anybody else’s place to chide you for calling it a “waste” – it was your time after all, and not mine. That said, I hope you can appreciate that we do hope to be kind to inquirers here, and I know from personal experience that something that is impressive to my non-expert, or wishful eyes in some area may well turn out to be obvious nonsense to those who know a lot more about it (or who did take more time to look into it). So I sure do appreciate when you do spell a few things out. Even if Raymond fails or refuses to be moved by your comments, bystanders like me still learn from your responses too. I knew nothing of these Google map tile artifacts or the claims that were triggered by those in the minds of some. So please don’t consider your time and effort a complete waste at any rate! And I suspect [know] I’m not the only one that follows these things here.


#143

In addition to the links Christy provided a couple of threads here are related.

Once you understand radiometric dating methods you will see that not all methods require a knowledge of parent/daughter ratios at the starting point.

You use more than one method that are based on different assumptions and note that in all cases the dates agree within the error bars. For C-14 articles of known age are dated and the dates agree.

You mean the YEC’s that lied about the origin of a rock when they submitted it for testing which caused the wrong dating method to be used?

This is not how index fossils are used to establish dates but it is the favorite way the YEC like to describe it as it certainly sounds dishonest. If interested you can Google it to see how they are really used.

A more helpful resource is The Bible, Rocks and Time by Christian geologists Davis Young and Ralph Stearley. It includes the history of geology and two chapters on radiometric dating methods.


(James McKay) #144

I think you may have missed @Bill_II’s point here. He was pointing out that different data sets are cross-checked against each other. When two different methods of measuring something give the same value, that is a pretty strong indicator that any underlying assumptions involved are reliable.

In some cases, you can establish limits on the starting point of the rock from its chemical properties. For example, zircon crystals can accept up to about 1% uranium or thorium, but never contain more than a few parts per trillion of lead, simply because lead atoms do not fit into their crystal structure.

In other cases, you can determine the age of a rock sample without needing to know anything about its original composition using a more advanced technique called isochron dating. This works by taking several different samples from a rock and plotting a graph of, for example, 87Rb/86Sr against 87Sr/86Sr. The maths is a little bit more complex but you can determine the age from the slope of the graph without needing to know anything about the original composition of your sample.

They greatly exaggerate the extent and significance of these bad dates.

It’s important to realise that there’s a vast difference between “doesn’t always work” and “never works.” What YECs don’t tell you is that these erroneous results are very much the exception rather than the rule, accounting for at most 5-10% of radiometric data overall. They also tend to imply that because dating method A doesn’t work on rock type X, that means that dating methods B, C and D don’t work on rock types Y or Z either. That simply doesn’t follow.

The fact remains that 90-95% of the time, different radiometric techniques give exactly the same results as each other within error bars. This simply wouldn’t happen if these techniques never worked, and certainly not if they were so out of whack that they consistently failed to tell the difference between thousands and billions.

Ah, the good old “fossils are used to date rocks and rocks are used to date fossils” shenanigan. An over-simplified and thoroughly dishonest straw man caricature of stratigraphy that bears no resemblance whatsoever to what real scientists actually do, and that completely misrepresents what constitutes circular reasoning and what doesn’t into the bargain.

Circular reasoning would be fossil A being used to date rock B and rock B then being used to date fossil A without any reference to any other form of evidence. What happens in reality is that rocks A, B, C, D and E (whose ages have been determined using radiometric and other techniques) are used to date fossils F, G, H, I and J of the same species, and then another fossil K of the same species is used to date rock L. Typically, the result is then cross-checked further using other index fossils, or other independent lines of evidence. That is not circular reasoning; it is inductive reasoning.

(For anyone who’s into graph theory, the lines of evidence do not form a circle; on the contrary, they form a directed acyclic graph.)


#145

Mervin, Your comment is well taken. I’ll confess that after watching that video, and doing the elementary but still time-consuming Googling of this and that, and composing a reply, I felt stupid for getting sucked into spending that much time on yet another pseudo-scientific video/article/book recommended by anti-evolutionists. I tried to resist the temptation to engage with this, but it was Saturday…

Anyway, I’m glad someone may benefit from my giving a fact-based response here, and I appreciate your reminder to stay gracious.


(Chris Falter) #146

If the radiometric dating method has an error bar of ± 500k years, then it can be very useful for dating a rock that is 50m years old. The standard error, expressed as a percentage of age, would be 1%.

Now suppose the rock is only 50 years old, but the method still has the same error bar of ± 500k years. What is the standard error of measurement as a percentage of age?

I am quite sure you can do the math yourself, Raymond.

Blessings,
Chris


(James McKay) #147

Hi Scott,

I’d agree that your taking the trouble to watch and respond to the video was welcome. However, I’d also say that you were right to rebuke @Raymond_Isbell for posting a 3/4 hour video in the first place. I’ve come to the conclusion over the years that a forum post should be able to stand alone on its own merits; external links and videos should only serve the purpose of telling people where you are getting your information from, and allowing them to fact-check what you are saying if necessary. Time is a limited resource for all of us, and expecting us to spend 45 minutes watching a video rather than just 2-3 minutes reading a summary of the key points is inconsiderate.


(Raymond Isbell) #148

Wow! I’m a little taken aback at the tone of the responses I’m getting from you guys. I offered the Jaye video as something of interest that takes a position that could be used by YECs to bolster their view of a young earth. I wanted to know your thoughts. It’s an academic discussion and you would think that Christians who take the opposite view would respond with a gracious and irenic tone that politely offers counter points and suggestions that outline a different way of interpreting the data. Instead, I get responses (not all, of course, but enough to wonder about the authenticity of their faith or the level of spiritual growth they’ve attained) that can be characterize as defensive, self-righteous, haughty, and what one would expect from non-Christians who feel threatened with any suggestion their beliefs might be wrong. Those kinds of response are typical of unbelieving evolutionists who feel threatened. One thing you would not expect from a Christian is an ad hominem attack. It’s interesting that in one day on Google you are now a world class expert on mapping and your understanding of it qualifies you to slam one who has spent his last 20 yrs working as a Systems Engineer and Research Scientist for the National Geospatial Intelligence Agency (NGA). I’ve been involved deeply in the design of satellite remote sensing and imaging technologies across the spectrum (not just electro-optical). I understand imaging artifacts and how images are seemed together subject to all the technical limitations that are possible. I was the lead Systems Engineer on the Shuttle Radar Topography Mission (SRTM) that flew in 2000 and generated a Digital Terrain Elevation Data (DTED) Level 2 Model of the earth between +/- 60 Deg latitudes. I worked with JPL for nearly 3 yrs to develop the payload sensor. In fact, I wrote a paper that saved the program from a proposal to use existing radar images and repeat pass interferometry as a substitute for the shuttle mission that would use a single pass interferometer which is essential to avoid temporal decorrelation in the old images. I have a pretty good understanding of how imaging from remote sensing is done. Looks like I could have learned more if I had just spent the weekend with Google or engaged in a BioLogos forum. Was your interpretation of that Google data eisegetical? Did you consider that the reason Google removed it was that the science can’t prove it either way? Putting something out on the internet that is so suggestive would be unwise because it could easily be slammed by critics giving Google a black eye. It’s amazing how you guys are so sure of a few facts like and old earth and evolution when there’s data and argument available that takes a different view. Jaye is making a case for a number of things but admits he can’t prove it. He shows some humility that I haven’t seen in this group (with a few nice exceptions of course). Your language toward my efforts to understand these issues is pretty strong. Here are some quotes from you: “But apparently you did not bother to check out this Google blog article yourself.,” “If you took the trouble to Google the subject of submarine canyons…,” “But you apparently did no follow-up here.,” “And if you had taken the slightest initiative towards your own critical examination of the extraordinary claims in this video you would not have wasted our time with it here.” In other words you are slamming me for not looking at your set of facts that 100% prove your position. By the way, I personally develop with a team of contractors a modernization plan for the Maritime Program at NGA to show the role that R&D could plan in bringing NGA’s maritime program into the modern digital age with new technology. I know and understand every phase of production of maritime mapping. I know about the various sensors that are employed, their use, their limitations, and how the raw sensor data is converted to Maritime products such as the Digital Nautical Chart (DNC).

One of the most interesting aspects of my engagement with you guys is how certain your are that you are correct even though it’s clear you don’t know fully how the cell works, how geology proves the earth to be old, etc. You have lots of research on micro-evolution that you extrapolate and conclude that macro-evolution is beyond dispute. Your defensive manner in engaging those who challenge you suggests a bit of insecurity. I suspect that each of you have some significant doubts about evolution, but evolution is so deeply ingressed in your thinking, and you and your reputations are so deeply invested in it that any challenge is taken as personal and potentially fatal to your identity. When you can’t challenge the facts from the other side, you resort to attacking the persons who are adducing them (ad hominem).

I will not let the “grumpiness” of some deter me from inquiring more. I really want to understand your thinking that leads you to accept evolution (macro that is). Let’s try to be kind and considerate even if you feel that you’re lowering yourself a bit to help one who is seeking answers. Remember the guidelines in the BioLogos forum: “Let your conversation be always full of grace, seasoned with salt, so that you may know how to answer everyone.” -Colossians 4:6 This is a place for gracious dialogue about science and faith.”


(Christy Hemphill) #149

In actuality I would guess the majority of the people who frequent this site were at one point in life YEC or ID proponents themselves and came to their current positions after some amount of painful reevaluating where they had to let go of some beliefs that were cherished to some degree. I agree the tone could be more cordial in many of these posts. But I don’t think it is correct to assume you are talking to a bunch of indoctrinated people who have never bothered to check out the claims of their other side. Many spent a good deal of effort trying to defend the other side until the preponderance of evidence eventually broke down their objections.

It is a free country and you can think what you want. But scientific consensus is not a conspiracy. It means something. One cannot hope to achieve the expert level proficiency in genetics, biochemistry, evolutionary ecology, geology, paleontology, and evolutionary anthropology that would be required to thoroughly and objectively evaluate all the claims of scientists against YEC and ID claims. At some point, you simply decide whom you trust and take their expert word for it.

Personally, I have seen enough YEC and ID claims that I used to accept flatly debunked at a level I could comprehend to find their experts untrustworthy and assume they are also wrong about the things I can’t comprehend. I’m not going to get a PhD in seven fields so I can understand all the details, I’m just going to trust the people who have proven trustworthy. One problem with YEC, and to a somewhat lesser degree ID, is that there often this implicit idea, that if something is valid, arguments for it should be accessible at the lay level and validated by intuition and common sense. That’s simply not true.

I second the reminder. Good for you persevering with your investigation.


(Christy Hemphill) #150

Oh please. This forum is littered with people posting 45 minute+ videos of debates, sermons, and other media, not to mention 40+ page scientific journal articles that certainly take more than an hour to actually read. No one is under any obligation to interact with a link just because it has been posted. The “stand alone” discussion guideline only applies to OPs. This thread is crammed full of external links you all expected Raymond to spend hours on educating himself. Don’t accuse someone of being inconsiderate because you find his link a waste of your time.

Skimming back through this thread, I’m surprised he’s still here at all. People have been pretty rude.


#151

@Raymond_Isbell If you are not following it there is another thread talking about macro-evolution.

I provided a link to a paper on the evidence for macro-evolution in whales which you might interesting.

https://www.researchgate.net/publication/262055002_Molecular_evolution_tracks_macroevolutionary_transitions_in_Cetacea


#152

Considering how skeptical you are (which is fine) about many other things, I was genuinely surprised that you did not seem to do rudimentary fact-checking on the extraordinary claims in Michael Jaye’s video (that a network of gigantic human-constructed canals lies at the bottom of the ocean, that the only explanation for submarine canyons is that the sea level used to be two miles lower, that plate tectonics cannot work). And I wanted to encourage you to do such fact-checking in the future.

But looking back at what I wrote, I realize it sounds like a personal attack on you, which was not my intention. I tend to be a just-the-facts kind of guy, often insensitive to how I come across. Please accept my apology, and feel free to correct any misstatements I may have made.


(Raymond Isbell) #153

Apology accepted. As I said earlier you look to be a good source for getting some tough questions answered so I look forward to more discussion.

One of the things I’ve learned about discussing topics with those who disagree with you is to recognize that we are all coming at it with a bag of information that’s incomplete, with bias, and a sense that the other person is attacking us. The latter often gets our hackles up and we say things that we may regret. Paul warns us in Rom 8:1 that knowledge puffs up (φυσιόω). We all need to be on guard that we don’t let that tendency manifest in our discussion with others. That said, let’s continue and let the world see God’s grace working in us as we strive to learn.


(Raymond Isbell) #154

Thanks Christy. I recognize that I may get under the skin of some with my “ignorant” questions, but in other areas, e.g., Systems Engineering, I know more than most others because I’ve had 30+ years working in the field on some pretty hard problems. My developed intuition from that experience tends to make me skeptical of the neo-Darwinian explanation for evolution. I’m not alone. As you know there are an increasing number of really smart folks (much smarter than me) who are recognizing the explanatory deficit of the neo-Darwinian explanation, e.g., the Nov 2016 Royal Society of London Conference organized to discuss the shortcomings of current evolutionary theory, and to find a new theory (extended evolutionary synthesis (EES)). Like you I listen and often heed the advice of others who know more. Given this I think it’s wise to engage with others who take the opposite view and learn about their reasoning to see why they are so confident when I and other see holes in it. Hopefully, since we’re all Christian and seek to honor our Lord and learn the truth, we can engage in a productive way that will bring us to common ground.


(Christy Hemphill) #155

I think it is a misconception that EES is a “new theory.” Saying neo-darwininian mechanisms don’t explain everything we observe is a far cry from throwing out the evolutionary model and “replacing” it. EES is grounded in evolutionary biology.


(Steve Schaffner) #156

In reality, a great deal is known about how cell functions are directed and coordinated. There is still a great deal to learn, of course, but enough pathways have been dissected in detail to have a very good idea of the kinds of ways that cells use for control purposes. For example, here is a reconstruction of one pathway, the insulin signaling pathway (taken from this paper):


The general pattern of cellular processes is clear: there is no central controller. As with processes like limb development, cellular processes run as semi-autonomous, loosely coupled modules.

You would get better results, and raise fewer hackles, if you would first ask what we know rather than telling us how ignorant and foolish we are.


(Raymond Isbell) #157

I don’t think I’ve ever said any of you is foolish. When I use the term ignorant, I don’t use it in a pejorative sense. I mean it as it regards our knowledge of the some of the more sophisticated operations of the cell. We (me more than you) are definitely ignorant of a lot of cell functions, aren’t we?

By the way, I acquired a book titled “An Introduction to Systems Biology” by Uri Alon. He makes the following statement in the Introduction (pg.5) “This information-processing function, which determines the rate of production of each protein, is largely carried out by transcription networks.” I’ve started reading it. Sounds interesting even though I sense there’s much more to the command and control function that these transcription networks. I’m also reading James Shapiro’s book “evolution - A View from the 21st Century.” The chapter on Sensing, Signaling and Decision-Making looks interesting and relevant to the C4 functions that must be present. I’m learning a lot.


(James McKay) #158

Well Raymond, you can consider me ignorant in this sense, because I’m not a biologist. I’ve a very rudimentary understanding of the basics of DNA transcription and protein encoding, but a lot of it seems deeply mysterious to me.

However, I do know that knowledge and understanding doesn’t always translate neatly from one field of study to another. My university degree is in physics; I’m a software developer by profession; I spent ten years working for the UK Parliament; and I now work in the travel industry. While there are areas of overlap between these different disciplines, in general they have completely different requirements and completely different ways of working – you can’t view the laws of Great Britain in the same way as you view the laws of physics, for example. Consequently I’d be very surprised if you can view cell biology as a sub-discipline of systems engineering.


(Steve Schaffner) #159

Good choice.

Your intuition is not going to be a reliable guide to biology.

Less good choice.


(Raymond Isbell) #160

The two sources I mentioned earlier address the similarities. Here’s a quote from Shapiro: “Thinking about genomes from an informatic perspective, it is apparent that systems engineering is a better metaphor for the evolutionary process than the conventional view of evolution as a selection-biased random walk through the limitless space of possible DNA configurations.”

Shapiro, James A… Evolution: A View from the 21st Century (FT Press Science) . Pearson Education. Kindle Edition.


(Raymond Isbell) #161

I forgot to mention. In my view, Systems Engineering is a tool and a useful framework to see how a system-of-systems is functionally integrated. It provides an organizational structure that allows insight into a system’s design and operation so that it can be maintained and/or modified. The cell is a system-of-systems with high levels of functional integration.