Protein Folding- Chance Or 'design'?

[BlackCat]

Thanks Sdelsolray, for bringing the peer reviewed claim to our attention. 

[sdelsolray]

Thanks Sdelsolray, for bringing the peer reviewed claim to our attention. 

You're welcome, BlackCat.  How are you coming on your analysis of Behe's IC claim?  Once done with that, you may wish to check out how Stephen Meyer (another Discovery Institute heavyweight) doubles down on IC in his pseudoscience writings, as well as his doubling down on William Dembski's "specified complex information" pseudoscience.  

 

You can boil down just about all of the Discovery Institute's output to an argument from incredulity with a side salad of the Watchmaker argument.  They sure are good at making it sound all "sciency" though.  They impress even themselves.

[BlackCat]

Sdelsolray, I think I've got to grips with the IC 'problem'.  When BAA posted that image of the buckminsterfullerene molecule (post 43), I could not deny that its structure is irreducibly complex.  I have to admit that when it comes to a more complex structure like the flagellar motor, I am still somewhat bewitched by its complexity, or rather the sum total of these machines that combine to form a machine like ourselves.  It is beyond my comprehension how they managed to form over time something as complex as us (or any other animal) but they did evolve and so I no longer jump to the God conclusion.  The buckminsterfullerene molecule is a good way to refocus my thinking.

 

I still wonder about God though, and probably always will.  This is no doubt down to not wanting to accept that this life is all there is and you aren't going to see loved ones again.  Maybe that is something that I will come to terms with over time.  It's taken me a lot of years to get free of religion and belief in a theistic God, and so some of my thinking (and longing) is still 'God' motivated I suppose. 

 

This is interesting: I came across this amazing Ted talk on you tube this morning.  Type in: ''Digital biology and open science-the coming revolution [stephen Larson} TEDxVienna''.  This guy touches on the same 'design inference' that molecular machines seem to have, but then he expands on this.  IT's a great talk. 

 

I've checked out Stephen Meyer.  He does make ID sound very convincing, as do the others. 

[ExCBooster]

See also the lovely PBS Nova special on that court case BAA mentioned. Watch the whole thing for free, here. (Especially the mousetrap/tie clip thing.)

 

Besides, protein folding (simplified video animation here) only works so wonderfully, sometimes. It's a terrible kludge, actually. Because at the point where it happens (DNA transcription to RNA, then RNA into proteins) it really IS just atoms experiencing chemical bonds, and wafting around randomly. Stuff goes wrong. Stuff goes wrong all the time. It's terribly inefficient, and mutations happen. It's just, fortunately, it's SO inefficient (most of the DNA doesn't even code for anything, or anything important), that most of these mutations don't really affect anything too badly. It's a chemical process, straight up, and we can even do it in a lab (where it goes a lot better than in a cell).

 

 

These are all of the things that are direct results of errors in the transcription process (and subsequent steps in cells interacting with proteins):

 

Prion diseases (literally mis-folded proteins)

Any genetic disorder ever (that's the definition)

Chromosome disorders (whole massive chunks of the code get misplaced in the process)

Viruses (scraps of RNA that hijack your cells' transcription processes)

Cancer. All of it.

 

Check out this list of leading causes of death, and compare to the above. Biological "mistakes" are incredibly likely to kill you. As in, way more likely than not.

 

Imagine, if you will, a car factory:

While the assembly line is running, about 10% of the time, half of the materials to make a car are missing, and no car is made at all.

Of the remaining 90%, only half of the cars even get finished.

Of that half that do roll off the assembly line, 1 in 33 have manufacturing defects (about 3%)

If you crunch the numbers, this car factory only produces a "healthy" car 43.65% of the time. 

Worst car factory ever: fire the CEO.

 

If you read the links, I was citing papers on human fertility. So, yeah - it's a tremendous misconception that evolution turns out complex things that are perfectly suited to their functions, even on a molecular level. The premise that it's all so elaborate, and it works so well, is just not true to begin with.

[BlackCat]

Hi ExCBooster, cheers for your input.  

 

I would have to disagree with you when you say: ''The premise that it's all so elaborate, and it works so well, is just not true to begin with.''  Please check the Ted talk I mentioned in my last reply (Digital biology and open science....).  I also recommend another one:  ''TEDxCaltech - J.Craig Venter- Future Biology.''  Both those talks really drive home how elaborate biological systems are and how they work so well.

 

Going back to the first TED talk by Stephen Larson, if you watch from 04:34 to 06:07.  He claims that current estimates for the error rate of DNA copying is 1 mutation for every 10 billion base pairs that are replicated.   He likens this error rate to the number of people who are thought to have ever lived: 100 billion people.  So if we were as good as DNA at transmitting information from generation to generation, then only 10 people in all of history have ever miscommunicated.  I'm not sure how this compares to the errors that you cite ExCBooster.  Maybe RogueScholar can help us there.  I'm not sure how much of these diseases and disorders are caused by things going wrong that are not down to the DNA (originally) but external influences.  Take cancer.  Many cancers are caused by external things e.g too much sun, smoking, bad diet.  

 

Guys, I'd like your opinion on the two TED talks I've mentioned.  Especially the first one.  Cheers.   

[RogueScholar]

BlackCat, these diseases you speak of are incredibly complicated. I have not watched the TED videos and I really do not have the time to go through them in any detail, but feel free to ask specific questions and I can try to answer. Regarding this mutation claim; while it is true that the error rate is very low, I think the intuition you took away from the statistic is not quite a good reflection of reality. You need to remember that DNA & RNA is being replicated, copied, translated, transcribed and so on all day long in virtually all of our metabolically active cells. So while errors are rare, these errors are going to occur in everybody simply due to the massive amount of "information" that is being copied and shuttled around our cells. In many cases, our cells have mechanisms that allow for limited repair of certain types of errors and in many cases, there are characteristic changes that occur in cells when "critical" errors occur that will activate a cascade of changes that basically causes the cell to kill its self (apoptosis) so it does not become a problem.

 

However, these mechanisms do not always work and if mutations involve cell growth and regulation, the cell may lose its ability to perform its job and begin dividing faster than normal. This is a precursor event to the development of certain diseases such as cancer. In many cases, the immune system can respond and eliminate these problems, but not always.

 

The genetics of cancer can get really complicated. We now know that there are certain genes that act to suppress cell growth and prevent cells from being cancerous. These so called "tumour suppressor" genes are important and if a mutation or some other error were to occur, these genes could be switched off, essentially increasing the risk of cancer. There are also other genes that are typically inactive but if mutated or acted upon, can become active and cause the cell to become cancerous. These are known as proto-oncogenes and when activated or expressed at higher than normal rates, will become oncogenes and increase the risk of cancer.

 

While certain external events such as ionising radiation exposure, many chemical and cigarette smoke among other things are associated with DNA changes that can lead to cancer, it looks like cancer is often the result of "dumb luck." Unfortunately, the process of normal cell energy production will cause cell damage. Cells basically break down organic molecules such as glucose and use the potential energy of the chemical bonds of these molecules as a way of "powering" cellular processes.  However, for this to occur, cells need to make use of reactive molecules. Oxygen is a key component of this process. Unfortunately, Oxygen is a highly reactive atom and is very good at causing so called oxidative damage. No matter how good the cell works, a certain amount of highly reactive molecules collectively known as reactive Oxygen species and free radicals will be produced. Normal cell detoxification processes are generally quite good at "neutralising" these reactive molecules, but eventually one of these guys will cause cell damage because so many are being produced and this process is ongoing. The will eventually cause progressive damage and breakdown. This is actually one of the major mechanisms of aging. Cells simply degenerate and their DNA degrades as a human ages due to these "normal" processes. So in a real sense, aging, death and concepts such as cancer are a natural consequence of cells making energy and surviving.

[Brother Jeff]

Intelligent Design is not science. Science is concerned with and deals with the natural world. Once you bring a supernatural being or claim into it, it ceases to be science. ID Theory is pushed by a small group of Christian fundamentalists who want to get their silly religious myths taught in public school science classes. It's nothing but Creationism 2.0, and a way for them to try to get god mentioned in science classes, which is exactly where he does not belong. Discussions about god belong in religion classes, not science classes.

 

[bornagainathiest]

Hi ExCBooster, cheers for your input.

 

I would have to disagree with you when you say: ''The premise that it's all so elaborate, and it works so well, is just not true to begin with.''  Please check the Ted talk I mentioned in my last reply (Digital biology and open science....).  I also recommend another one:  ''TEDxCaltech - J.Craig Venter- Future Biology.''  Both those talks really drive home how elaborate biological systems are and how they work so well.

 

Going back to the first TED talk by Stephen Larson, if you watch from 04:34 to 06:07.  He claims that current estimates for the error rate of DNA copying is 1 mutation for every 10 billion base pairs that are replicated.   He likens this error rate to the number of people who are thought to have ever lived: 100 billion people.  So if we were as good as DNA at transmitting information from generation to generation, then only 10 people in all of history have ever miscommunicated.  I'm not sure how this compares to the errors that you cite ExCBooster.  Maybe RogueScholar can help us there.  I'm not sure how much of these diseases and disorders are caused by things going wrong that are not down to the DNA (originally) but external influences.  Take cancer.  Many cancers are caused by external things e.g too much sun, smoking, bad diet.  

 

Guys, I'd like your opinion on the two TED talks I've mentioned.  Especially the first one.  Cheers. 

 

BC,

 

Are you thinking skeptically about this?  

Please try to remember that for a skeptic, the default position on all matters is one of disbelief.  Not belief. Therefore, until you have weighed as much of the evidence as you can understand, isn't it premature for you to say that you disagree with ExCB's statement?

 

Your disagreement doesn't stem from a balanced review of the evidence, does it?

Because you are still trying to get a handle on this difficult and complex subject and because you are asking the RogueScholar for his input.  So you really can't have reached the point where you can say that you disagree - on the basis of the evidence.

 

I'd hazard that you still find these molecular machines too fascinating and too appealing to treat as merely blind assemblages of atoms.  That at some deep level, they still suggest to you 'something' that smacks of design and intelligence.  Hence your premature disagreement with ExCB.  Which isn't skeptical and isn't evidence-based, but is probably rooted in some personal need or preference for some kind of cosmic purpose.

 

Please note BC that true skeptics try to identify these needs within themselves and then put them to one side.

Personal biases, preferences and needs play no role in skeptical thinking and we must do our level best to combat them whenever and wherever they occur.

 

Once again BC, I don't write these things to chide you or put you down.

You asked us to step in when you slipped into the wrong kind of thinking and I suspect this is what's happening with your all-too-quick disagreement with ExCB.  

 

I hope you take my words in the spirit they are intended.

 

Thanks,

 

BAA.

[BlackCat]

Brother Jeff, thanks for posting that film.  Good points. 

 

 

BAA- I smiled when I read your post.  You know I appreciate your honesty.    

 

Let me start by asking a question first.  Did you watch those two short films I mentioned?  The first one is a must, but ideally the two of them as the second one drives home many points made in the first?  It's important that you have watched them, as I will be referring to them when I answer your specific questions and points.

[Brother Jeff]

Couple of good videos on ID from Daniel Dennett and Neil deGrasse Tyson:

 

https://www.youtube.com/watch?v=EFwnjD68HSc

 

[BlackCat]

Brother Jeff, it just so happens I'm about to tackle a mountain of ironing, so I shall pop the Neil DeGrasse Tyson one on.  Cheers.

[BlackCat]

RogueScholar, thank you for explaining some of the processes that cause mutations, diseases, etc. It's a shame you aren't able to watch those videos, the first one in particular. I'll come back to your reply when I further discuss this with BAA.  Cheers again.

[RogueScholar]

Feel free to ask questions. I do not believe that I really need to watch specific videos because I am going under the assumption you have well developed questions and have thought about the concepts presented? For example, I watch a video on chemical bonding and have specific questions about something that was stated. I would not mandate somebody watch the video and then get back to me with their thoughts, but rather I would think about the issue and present questions or conclusions based on my own ideas and research that other people could discuss without having to marathon through entire videos. After all, this discussion is about you and your thoughts and beliefs, so I would rather deal directly with your ideas. However, I am familiar with Ken Dill as he is one of the leading biophysics researchers working on protein structure. One thing I would caution is that he likely makes many metaphors and I bet he likely says that these "machines" are not at all like the machines that you intuitively understand. Hopefully that makes sense?

[BlackCat]

RogueScholar, life is made up of very complex processes e.g. molecular machines.  This is a well established fact would you not agree?  If anyone was in any doubt about  that then I recommend (like you did for me with the chemical evolution video) that they watch the first video I mentioned with Stephen Larson.  It's only 19 minutes long.  I have been advised to read various articles and watch videos by different members for the same reasons I recommend the video of Stephen Larson.  No big deal.  I urged BAA to watch it, specifically because he accused me of going under the spell of ID again and of not employing scepticism.  If he watches the Stephen Larson video he will hopefully understand better,  the points I was trying to make and hopefully see that he was mistaken in what he believed about me.

 

 

There were three reasons I found that video (and the other I mentioned) so interesting:

 

1. They clearly demonstrate how beautiful (i.e. equations must be beautiful) molecular structures are.  They are indeed complex. 

 

2. We are learning how these molecules are put together and how molecular machines work and how efficient they are, and the more we learn about how they work the more we can confer those efficiencies over to our man made systems e.g renewable energy.

 

3. What those two videos demonstrated was NOT intelligent design.  The videos show how we are unlocking the mysteries of life and so they have helped to cement the realisation (for me) that life is purely down to natural processes and an intelligent designer is not needed. 

 

The first two points answer why I disagreed with ExCBooster.  The third point was why I mentioned the video in the first place.

 

So, I was not leaning back towards ID, when I said I am still bewitched by molecular machines.  I am and no doubt always will be utterly awestruck by the beauty and complexity of life.  It's ok to look at life and see 'design'.  I now know that the 'design' has happened very slowly, over billions of years by natural processes.  It has not been designed.  When we copy nature's systems, we have to design the copies, as we haven't had the billions of years of slow development that nature has used.  I understand that now. 

 

Brother Jeff linked to some very pertinent videos.  The one by Neil DeGrasse Tyson really hit home how lucky we are to be alive.  He also takes you through the centuries and shows how the great minds of the past only brought the Designer into the equation once they'd reached the limits of their understanding.  As knowledge increased, God was brought in further down the line.  It's a great talk and again, it cemented many new truths for me.  I managed to watch two third of the Daniel Dennett one ( I had a lot of ironing), and that was very much appreciated, as he drove home the faulty thinking that leads to believing intelligent design.  Thanks again Brother Jeff.

[bornagainathiest]

Hi BC!

 

I will be making some time to look at those videos and will get back to you accordingly.

 

Thanks,

 

BAA.

[BlackCat]

Cheers BAA, appreciate that.  Looking forward to your thoughts on them.