Darwin Unhinged: The Bugs in Evolution

...........................................

Nevertheless, I'd still urge StephenW to realise that there really is a huge problem accounting for the digital information stored in genes.

Let us say you want the information to build an enzyme of some sort. The active site of an enzyme will bring a number of amino acid residues into close proximity, where they can interact with the substrate of the enzyme to catalyse some chemical transformation. The problem is that these residues will not typically be adjacent on the linear chain of the protein, they will only become adjacent after the linear protein chain has folded up - an enormously complicated subject, that is not well understood. So creating the information in a novel gene is only possible by an entity that understands this whole process completely. You can't circumvent this process. Remember that equations could be laid out as strings of symbols using the same encoding process, so if there were a way to magically create the information in a gene, you could equally well generate all the equations of QM or advanced maths using the same process!

If you can't rely on RM+NS, you have to have a consciousness that understands the whole biochemical problem.

This is really big, but it's just part of the problem. The genes primarily encode the protein building blocks of the organism. There is also the origin of the huge bulk of information directing the process of development of the organism. 

DNA is a linear code of molecules that just creates another linear set of molecules, amino acids which fold up into protein molecules having a myriad of functions. But this is just a small piece of a four dimensional exceedingly complex puzzle. The cell and the organism are three dimensional and the genome has no information to handle this. Then it turns out that it is actually a four dimensional puzzle because timing and sequencing are necessarily added on top of this - all the stored information determining the time sequence of development, when, how and also where each specialized cell must be built and then migrate to form various stages in building up the embryo. 

Much or most of the spatial and time sequence information to form an embryo appears to be specified independently of the DNA. There is some noncoding DNA. The coding and storage of all this information appears not to be much understood as of yet. It is known that there exist codes in the cell membranes called sugar codes and bio electric field codes. There are probably other codes too. So DNA is just one form of a biology code and may be a relatively simple one compared to the others. 

I would contend that creating all this coded information for the specialized cell types and construction, 3-D spatial arrangements of cells, and time sequences required to build the organism is also only possible by a conscious entity that completely understands the whole embryological development process. I think there is overwhelming evidence that it can't be RM & NS.

Me too. Here's the abstract:

Word salad in a super-specialized esoteric jargon. 

First, let me say I appreciate you trying to learn about the subjects.  You have cited Gordana Dodig-Crnkovic presenting a paper entitled: "Floridi's informational structural realist basis for info-computational modelling of cognizing agents."

She is not describing an overview of Floridi's positions, but specific concepts important in making robots work.  I have read this paper.  It is full of jargon that is useful to technical folks working on the project.

First, let me say I appreciate you trying to learn about the subjects.  You have cited Gordana Dodig-Crnkovic presenting a paper entitled: "Floridi's informational structural realist basis for info-computational modelling of cognizing agents."

She is not describing an overview of Floridi's positions, but specific concepts important in making robots work.  I have read this paper.  It is full of jargon that is useful to technical folks working on the project.

I think the most interesting question for me would be if there are people actually building robots who reference Floridi's work, or if there are people working in the Third way Movement who are referencing his work. I don't need to re-state the scepticism both nbtruthman and I feel towards Floridi.

In the meantime, I'd love you to watch this video by Professor James Tour. He has done a lot of remarkable research into nano-machines (basically assemblies of large molecules), and he is interested in how this work relates to the origin of life. It explores far more than the question of where the information in DNA came from. For example, he points out that organic chemists do chemistry one step at a time (mostly), purifying the chemicals between steps, and they use precise conditions such as the temperature of the reagents. Often they have to run a reaction for a certain amount of time at a high temperature before rapidly cooling it (quenching) to stop the reaction going too far. All of this is another form of information if you like, and it has to be got just right to assemble the molecules of life in a lab.

https://youtu.be/zU7Lww-sBPg

He can hector a bit, but it really is worth watching

Obviously this relates to that first step - the origin of life - but that is clearly related to the subsequent step - the evolution of life once it is started. He is clearly rightly exasperated by those that glibly stack up sequences of chemical reactions that work (often with very poor yields) in a lab, and assume they could have worked in hot pools on the pre-biotic Earth. Purifying intermediate chemicals is crucial, because unwanted biproducts build up and react with the desired chemical in unfortunate ways. This can often end up as a brown gung that organic chemists refer to as 'tar'!

James Tour is a pretty fanatical Christian, so he interprets all this as proof that God created life on earth. However, as nbtruthman pointed out, all it really is, is evidence that some very intelligent entity/entities worked on the problem.

I think the most interesting question for me would be if there are people actually building robots who reference Floridi's work, or if there are people working in the Third way Movement who are referencing his work. I don't need to re-state the scepticism both nbtruthman and I feel towards Floridi.

James Tour is a pretty fanatical Christian, so he interprets all this as proof that God created life on earth. However, as nbtruthman pointed out, all it really is, is evidence that some very intelligent entity/entities worked on the problem.

Thanks for the link.  James Tour, as an individual scientist is new to me.  WOW.  I will follow his work and biography from now on.  His practical output is outstanding.  

Floridi and Tour are in different arenas.  It would be James Tour whose work would be practical in building robots and not Floridi.  Floridi - and those who find his work profitable - may help AI scientists model biological mind.  Whether Floridi's ideas will make a difference, will have to be in determined in the future.

James Tour should be getting more notice, as a scientist, and it may be because of his active religious stance.  That should not matter.

DNA is a linear code of molecules that just creates another linear set of molecules,

I have to address this because it is such a crucial fact - DNA is not linear -  as a potential source of a chemical signal or in its activity as information.

 Why is DNA a dynamic structure?

It is dynamic with high energy. It exists naturally in a slightly underwound state and its status changes in waves generated by normal cell functions such as DNA replication, transcription, repair and recombination

Stay with sources like James Tour.  Is this something he said?

Thanks for leading me to James Tour.  https://creation.com/images/pdfs/tj/j26_..._70-72.pdf


https://www.youtube.com/c/DrJamesTour/videos




...

Watched Tour's video (nearly in its entirety).  He's an engaging speaker for sure.

I googled to see what counter-responses might exist.  Looks like he was critiqued by a youtuber "Professor Dave Explains".  Seems he sees Tour's criticisms of abiogensis to be disingenuous.  I only watched a snippet or two from his videos.  Unfortunately, while he criticizes Tour for his religious beliefs while insisting its okay for Tour to have religious beliefs, he fails to acknowledge how his own metaphysical worldview might impact his criticisms.

That said he does appear to have contacted many of the scientists that Tour took issue with.  If anyone's interested, see below:

https://www.youtube.com/watch?v=SixyZ7DkSjA&t=243s

https://www.youtube.com/watch?v=ghJGnMwRHCs&t=178s

https://www.youtube.com/watch?v=Jf72o6HmVNk

Watched Tour's video (nearly in its entirety).  He's an engaging speaker for sure.

I googled to see what counter-responses might exist.  Looks like he was critiqued by a youtuber "Professor Dave Explains".  Seems he sees Tour's criticisms of abiogensis to be disingenuous.  I only watched a snippet or two from his videos.  Unfortunately, while he criticizes Tour for his religious beliefs while insisting its okay for Tour to have religious beliefs, he fails to acknowledge how his own metaphysical worldview might impact his criticisms.

That said he does appear to have contacted many of the scientists that Tour took issue with.  If anyone's interested, see below:

https://www.youtube.com/watch?v=SixyZ7DkSjA&t=243s

https://www.youtube.com/watch?v=ghJGnMwRHCs&t=178s

https://www.youtube.com/watch?v=Jf72o6HmVNk

Let's just take the first issue you raise. I think it is obvious that when James Tour says, "We don't know how to make even the simplest of the biological monomers" he obviously means that we don't know how to propose that these are created naturally on the earth before life existed. I think this is important, and later on he also points out that these molecules are quite reactive, and it is incredibly implausible that even if the odd one formed, that they would build up into useful quantities of chemical starting points.

To appreciate how stupid the idea of random chemistry really is, you really have to have done some organic chemistry. The real problem is that it is all too easy to get organic molecules to react together, and cross link like crazy to produce what chemists refer to as 'tar'.

Clipped on to this is a complaint that Tour's research is unrelated to the start of life - but in a way, it is supremely relevant, because he researches ways to create nanobots - molecules that do things like roll forwards on tiny wheels, or in other ways. This research shows how incredibly hard it is to make such systems, and how much intelligent design (from his own mind) needs to go into creating even very simple nanobots.

I think it would be fun to listen to a debate between James Tour and 'Professor Dave', but as it is, he is (I presume) anonymous - so he can say what he likes.

I have to address this because it is such a crucial fact - DNA is not linear -  as a potential source of a chemical signal or in its activity as information.

Well it is a spiral chain of nucleotide bases, and in itself is nothing more. I mean it is only active in the sense that other molecules - proteins of various sorts -interact with it.

It is linear in the same sense that a human sentence is linear.

I think it would be fun to listen to a debate between James Tour and 'Professor Dave', but as it is, he is (I presume) anonymous - so he can say what he likes.

I don't think it would be that interesting.  This "Professor Dave" appears to be an internet personality and as such I don't see him as a SME.

I'd much rather see a thoughtful scientist working in and supportive of abiogensis respond to Tour's criticisms.  As you find them compelling, I do as well albeit I am a true layman when it comes to the related sciences (e.g., organic chem, etc.).

Professor Dave was the only critic I could find in a, granted, very quick search.

I wish there were more debates on topics like this.  As I've mentioned before, I found the Sam Harris and Jordan Peterson long form debates to be of great interest.  Both were respectful of the other, but attacked each other's ideas with vigor.  I know its an unrelated topic, but the structure/form of the debate is the point.