falsifying Natural Selection

[Ronja]

Spinoza: you noted "blind obedience to an unbreakable physical law" as one possible power behind movement. However, you forgot to answer this question, which is a crucial one:

There is no knowledge involved in any of these [simple, chemical or electro-magnetis] cases - so why should there be knowledge involved in more complex biochemical reactions or bonds? Where exactly would "knowledge" enter the picture, when we move from simple, basic chemical reactions and bonds towards more complex, biochemical ones, and what evidence can you present for that?

If you want to claim "knowledge" as some kind of causation-capable power, you have to be able to explain how the movement / arrangement of DNA/RNA is seriously different from movement based on physical laws (electromagnetism most often being the base group of phenomena involved). Why would DNA/RNA formation require anything more than the usual (bio)chemical phenomena as its base? Evidence, please!

[GenesForLife]

Thanks for the free microbiology book, I've just downloaded it and look forward to reading it. If you know of a free organic chem or biochem textbook, let me know.

Erm, it is Molecular Biology.

I am uploading Lehninger's Principles of Biochemistry at the moment and will post the link as and when it is done. I used Morrison & Boyd for organic chemistry but it was a miserable old hard copy.

[GenesForLife]

Base pairing is just chemistry, electron tunnelling has been directly observed

Molecular tips in scanning tunneling microscopy can directly detect intermolecular electron tunneling between sample and tip molecules and reveal the tunneling facilitation through chemical interactions that provide overlap of respective electronic wave functions, that is, hydrogen-bond, metal-coordination-bond, and charge-transfer interactions. Nucleobase molecular tips were prepared by chemical modification of underlying metal tips with thiol derivatives of adenine, guanine, cytosine, and uracil and the outmost single nucleobase adsorbate probes intermolecular electron tunneling to or from a sample nucleobase molecule. We found that the electron tunneling between a sample nucleobase and its complementary nucleobase molecular tip was much facilitated compared with its noncomplementary counterpart. The complementary nucleobase tip was thereby capable of electrically pinpointing each nucleobase. Chemically selective imaging using molecular tips may be coined “intermolecular tunneling microscopy” as its principle goes and is of general significance for novel molecular imaging of chemical identities at the membrane and solid surfaces.

http://www.pnas.org/content/103/1/10.full

Tunneling co-ordination ensures that complementary base pairing is the more stable configuration due to stronger bonding and overlapping of bonding interactions.

[Feck]

As always the answer to anything about science you don't understand is study more science .The answer to things science does not understand yet is, wait we are getting there .

At no point is 'God makes it happen ' or any other variant of that thought valid .Almost everything was irreducibly complex a thousand years ago and little is now not almost completely understood . All through this thread Spinoza you have been trying to get 'I do not know' as an answer I would suggest that if that is your quest then try asking about cosmology not biology . The main point that you are missing is that the non existence of a definitive scientific answer (yet) to a question in no way lends any credence to the idea of a god or designer . You are expecting science to explain EVERYTHING ,NOW ! which is a strawman . Even if you can stump Genes with a question about biology (good luck with that BTW) You are the one making claims that so far have been disproved in general and in particular every time they are investigated . When you can present any evidence for a designer then sensible people will listen and study it.At the moment you and the rest of the Godunit crowd are still desperately trying to claim a gap in current human knowledge PROVES God .

[spinoza99]

A r e y o u s e r i o u s l y p o r t r a y i n g a c a r i c a t u r e w h e r e t h e r e i s j u s t o n e m R N A m o l e c u l e , j u s t o n e r i b o s o m e a n d j u s t s o m e a m i n o a c i d s a n d j u s t s o m e t R N A t h a t c a n o n l y m e e t a n d c a r r y o u t r e a c t i o n s i n o n e p l a c e ?

T h e g r e e n b i t i s t h e e n d o p l a s m i c r e t i c u l u m a n d r i b o s o m e s a r e b o u n d t o i t , a n d i t e x t e n d s a l l o v e r t h e p l a c e .

You're not answering the question. Here is what you just did. I asked you the equivalent of how does an acrobat balance himself on a highwire and you said, other acrobats can balance on other highwires. What I am asking you is how to these GTFS know where to go. They all play a role and they do it. How do they do it. You didn't answer the question.

W e ' r e t a l k i n g a b o u t t h e t i m e p e r i o d b e f o r e t h e e x i s t e n c e o f c e l l s . Y o u h a v e t o b u i l d a c e l l b e f o r e y o u c a n g e t g e n e s . I n o r d e r t o b u i l d t h e f i r s t c e l l t h a t e v e r e x i s t e d y o u n e e d p r o t e i n s , a s w e l l a s a l l t h e o t h e r 4 0 o r 5 0 p a r t s o f a c e l l . Y o u c a n ' t b u i l d t h o s e p a r t s w i t h n a t u r a l s e l e c t i o n . [ / q u o t e ]

I s h o w e d t h a t s e l f r e p l i c a t i n g e n t i t i e s c a n f o r m w i t h o u t p r o t e i n s , a n d o n e o f t h e c a s e s t u d i e s i n c l u d e d [ i ] R i b o z y m e s t h a t c a n m a k e p e p t i d e b o n d s , t h u s p r o d u c i n g p r o t e i n s w i t h o u t r i b o s o m e s a n d o t h e r t h i n g s [ / i ]

What do you think these ribosomes are composed of and what are the proteins composed of that they produce, just give me the number of amino acids.

N o b o d y i s s a y i n g t h a t a b i o g e n e s i s i s c o m p l e t e l y r e s o l v e d e t c e t e r a , a n d i t i s a n a r e a o f r e s e a r c h t h a t i s v e r y m u c h p r o g r e s s i n g , b u t n o e v i d e n c e a t t h e m o m e n t f o r t h e r e q u i r e m e n t s o f b a s i c l i f e p r o c e s s e s s u g g e s t s t h a t n a t u r a l p r o c e s s e s a r e i n a d e q u a t e ,

Let's just try to figure out what you believe are the essential elements needed for constructing a cell and let's try to figure out what the minimum odds for their formation are. Go ahead and tell me what components need to exist in order to form the first cell. Moreover, I see no reason why these protocells are not around today. Prokaryotes are around, why not the other protocells. If these protocells are so easy to form why aren't they alive today?

I guarantee you the odds will be well beyond one and a hundred googols but atheists never want to try to calculate odds because they know that the odds are against them.


i n f a c t , a l o t o f t h e f u n c t i o n s i n v o l v e d , i n c l u d i n g r e p l i c a t i o n a n d p e p t i d e s y n t h e s i s , e v e n w i t h o u t r i b o z y m e s , h a s a l r e a d y b e e n d e s c r i b e d .


[ q u o t e ]
p r o t e i n s y n t h e s i s i s i n f a c t r e d u c i b l e t o t h i s

P e p t i d e b o n d f o r m a t i o n b y t h e r i b o s o m e r e q u i r e s 2 3 S r R N A a n d i t s i n t e r a c t i o n w i t h t h e 3 2 - C C A e n d o f t R N A .

Just forming one ribosome is far from easy. A ribosome in a prokaryote is composed of the following: Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit. Their large subunit is composed of a 5S RNA subunit (consisting of 120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 34 proteins. The 30S subunit has a 1540 nucleotide RNA subunit (16S) bound to 21 proteins.

The odds of arranging 1540 nucleotides are well beyond one in 10^200.

[spinoza99]

As always the answer to anything about science you don't understand is study more science .The answer to things science does not understand yet is, wait we are getting there .

Feck, do you really believe that? Science has discovered some answers, therefore it can discover ALL answers. Do you really believe that?

[GenesForLife]

Of course, I do not know is not a valid answer. Picture this.

"Mr.A"
"Yes m'lord"
" Did your daughter sleep with Mr.B last night "
"I do not know, m'lord, and I cannot be sure"
Judgement "Therefore Mr.C is declared guilty of sleeping with your daughter despite there being no evidence for it"

[GenesForLife]

Diffusion and dispersion, mRNA, tRNA and rRNA are all made in the nucleus in Eurkaryotes. They tend to move from regions of higher concentration to lower concentration with time through the medium which is all round the cell, amino acids are found in the cytoplasm and enter the ER through passive diffusion. Both of which are again elementary chemical processes.

With bacteria it is even simpler, there is no distinct nucleus so everything floats around and works by the same principles.

[spinoza99]

There is no knowledge involved in any of these [simple, chemical or electro-magnetis] cases - so why should there be knowledge involved in more complex biochemical reactions or bonds? Where exactly would "knowledge" enter the picture, when we move from simple, basic chemical reactions and bonds towards more complex, biochemical ones, and what evidence can you present for that?

The evidence lies in the odds. The general transcription factors are moving in precise locations. They are not moving like Brownian Motion. They cannot be obeying laws of their properties because it is not a property of an object: ok, when this amino acid gets in this location and that amino acid gets in that location, I will get in this location. We know this because although that happens the same amino acid that has that composition will act in a different way.

As for knowledge, do you believe that Beethoven writing his 9th symphony is the result of bio-chemical processes?

[Feck]

As always the answer to anything about science you don't understand is study more science .The answer to things science does not understand yet is, wait we are getting there .

Feck, do you really believe that? Science has discovered some answers, therefore it can discover ALL answers. Do you really believe that?

No I think there are some things that we cannot experiment with ..quantum physics , string theory etc so we will only ever be able to theorise about and we may never find a definitive answer . Either you just missed my point or your canard is becoming your petard .

Thus the lies needed for ID are founded ! , Are you saying that anything we don't have an answer for Proves god ? Because it also proves FSM teapots and Unicorns if they are your particular little quirk .

[GenesForLife]

The precise location you speak of exists throughout the cytoplasm in prokaryotes and throughout the endoplasmic reticulum, which occupies a very large part of the Eukaryotic cell, in Eukaryotes, drop that canard immediately.

In a very few cases there are other physical processes such as carrier mediated confinement and retention/confinement, but evidence is that most of the movement is diffusive.

Optical imaging of single biomolecules and complexes in living cells provides a useful window into cellular processes. However, the three-dimensional dynamics of most important biomolecules in living cells remains essentially uncharacterized. The precise subcellular localization of mRNA-protein complexes plays a critical role in the spatial and temporal control of gene expression, and a full understanding of the control of gene expression requires precise characterization of mRNA transport dynamics beyond the optical diffraction limit. In this paper, we describe three-dimensional tracking of single mRNA particles with 25-nm precision in the x and y dimensions and 50-nm precision in the z dimension in live budding yeast cells using a microscope with a double-helix point spread function. Two statistical methods to detect intermittently confined and directed transport were used to quantify the three-dimensional trajectories of mRNA for the first time, using ARG3 mRNA as a model. Measurements and analysis show that the dynamics of ARG3 mRNA molecules are mostly diffusive, although periods of non-Brownian confinement and directed transport are observed. The quantitative methods detailed in this paper can be broadly applied to the study of mRNA localization and the dynamics of diverse other biomolecules in a wide variety of cell types.

http://www.pnas.org/content/107/42/17864.full

There is also emerging evidence for the mechanistic processes of microtubule contraction driving mRNA transport.

I cannot access the paper though, but here is another example.

Abstract

Intracellular mRNA localization is a common mechanism of post-transcriptional regulation of gene expression. In a wide range of organisms, mRNA localization coupled with translational regulation target the proteins to their site of function. Here, we describe recent exciting evidence that some mRNAs are transported as particles along the cytoskeleton by the molecular motors dynein, kinesin or myosin. We discuss the key questions of how localized mRNAs might be linked to motors and what determines their cytoplasmic destinations.

http://www.sciencedirect.com/science?_o ... archtype=a

In some other cases, it appears to be a combination of the two, especially during embryogenesis.

* posterior body axis and germ cell function. While nanos RNA is synthesized by the ovarian nurse cells and appears at the posterior pole of the ooctye late in oogenesis, the mechanism by which this RNA is translocated to and anchored at the oocyte posterior is unknown.Results: By labeling endogenous nanos RNA with GFP, we have been able to follow the dynamic pathway of nanos localization in living oocytes. We demonstrate that nanos localization initiates immediately upon nurse cell dumping, whereby diffusion, enhanced by microtubule-dependent cytoplasmic movements, translocates nanos RNA from the nurse cells to the ooctye posterior. At the posterior, nanos is trapped by association, in particles, with the posteriorly localized germ plasm. Actin-dependent anchoring of nanos RNA complexed to the germ plasm at the posterior maintains localization in the face of rapid cytoplasmic movements.Conclusions: These results reveal a diffusion-based, late-acting posterior localization mechanism for long-range transport of nanos mRNA. This mechanism differs from directed transport-based localization mechanisms in its reliance on bulk movement of RNA.

http://www.cell.com/current-biology/ret ... 2203004512


So, there are several mechanisms in current cells, but most cases appear to involve good old diffusion, it is of course an evolutionary favorable phene should something stemming from a genomic network regulating intracellular sublocalization enable an organism to develop more specialized morphology.

[GenesForLife]

And oh, Spinoza99, http://www.cell.com/current-biology/ret ... 2203004512

[Ronja]

... what evidence can you present for that?

The evidence lies in the odds. The general transcription factors are moving in precise locations. They are not moving like Brownian Motion. They cannot be obeying laws of their properties because it is not a property of an object: ok, when this amino acid gets in this location and that amino acid gets in that location, I will get in this location. We know this because although that happens the same amino acid that has that composition will act in a different way.

Could you please clarify the statement/claim that is bolded and colored in the quote? Especially the word "it" throws me off - what does that "it" reference to / signify?

[GenesForLife]

Spinoza, here is the Biochemistry textbook.

http://www.4shared.com/document/11OhNS0 ... ioche.html

[spinoza99]

The precise location you speak of exists throughout the cytoplasm in prokaryotes and throughout the endoplasmic reticulum, which occupies a very large part of the Eukaryotic cell, in Eukaryotes, drop that canard immediately.

Look, during transcription all these GTF have to work in coordination with each other and they have to know where they're going. What you just said is similar to saying that they have to go to a baseball stadium but if you would watch the video carefully they have to go to a precise location in the baseball stadium, it's as if they have to find the right seat in the stadium. How do they know how to do this?

I also never got answers about what you think the basic building blocks are for the construction of the first cell.