falsifying Natural Selection

[spinoza99]

Much of that coordination is the result of
instinctive-based and deeply routine reactions to automatic observations of other people's movements, postures, trajectories and speeds of movement, tone and loudness of voice, etc, etc.

Could you give some precise examples? And could you also tell me where you stand on whether you think Beethoven's 9th is the result of physical processes

[Ronja]

...Until one has thought hard about the immensity of geological time and the vast number of self-replicating molecules, the ability of selection to blindly fashion such intracacies must seem like an affront to reason. Dan Dennet's "Darwin's Dangerous Idea" deals very nicely with the philosophical questions which arise in this area.

Fully agreed. DDI freed me to let go of any residual "what if" thinking, because it clearly showed how the illusion of a permanent soul or consistent consciousness were not really needed for understanding human thought and emotion.

[Feck]

What are the odds of sodium chloride molecules in solution by random chance all arranging themselves to form A cube ?

Random chance strawman is strawman ! calculating the odds of a process that is not random is about as pointless as most of your thoughts .

[GenesForLife]

If one is wondering about the three dimensional structure of proteins, it boils down to some complicated chemistry, and that is that, including hydrogen bonding, hydrophobic and hydrophilic interactions, and substrate binding. This is the reason we can use nothing more than the sequence of a protein to predict its structure and function, there are tools such as I-TASSER which involve what we call ab-initio or "from scratch" modelling

GFL, I heard somewhere that some proteins have more than one possible structure after folding. Can you illuninate this, just out of interest?

Yup, this is true. Apparently this has something to do with the nature of protein folding, which according to the paper I link to, is the consequence of proteins randomly meandering through several conformational states before arriving at the most energetically favorable state, I need to study more about the dynamics of the process including what is known as the molecular chaperone system.

But for the moment I will leave you with that paper and one medically relevant case.

http://chekhov.cs.vt.edu/PAPERS/Dobson.Misfolding.pdf

& this, from a Nature paper I managed to pinch off google scholar.

Much evidence supports the hypothesis that the infectious agents of prion diseases are devoid of nucleic acid, and instead are
composed of a specific infectious protein1. This protein, PrPSc, seems to be generated by template-induced conformational
change of a normally expressed glycoprotein, PrPC (ref. 2). Although numerous studies have established the conversion of
PrPC to PrPSc as the central pathogenic event of prion disease, it is unknown whether cellular factors other than PrPC might be
required to stimulate efficient PrPSc production.We investigated the biochemical amplification of protease-resistant PrPSc-like
protein (PrPres) using a modified version3 of the protein-misfolding cyclic amplification method4. Here we report that
stoichiometric transformation of PrPC to PrPres in vitro requires specific RNA molecules. Notably, whereas mammalian RNA
preparations stimulate in vitro amplification of PrPres, RNA preparations from invertebrate species do not. Our findings
suggest that host-encoded stimulatory RNA molecules may have a role in the pathogenesis of prion disease. They also provide
a practical approach to improve the sensitivity of diagnostic techniques based on PrPres amplification.

They postulate that in the presence of an abnormal or misfolded protein, RNA based chaperoning mechanisms may result in normal proteins being misfolded too.

There is a simpler case study with respect to structure, too, most proteins can be denatured by deviant environmental conditions from which they have evolved and have naturally been selected in, for instance, try running PCR with normal polymerases and the enzyme can go kaput at the temperatures involved, Taq DNA polymerase works well at that temperature. Denaturation involves breakdown of protein structure, which can give you a hint about the link between sequence, structure and the environment.

I will try to start a new thread on protein folding soon after collecting more papers on the subject, which is not something I'm extremely familiar with.

[Ronja]

... And could you also tell me where you stand on whether you think Beethoven's 9th is the result of physical processes

If you want to discuss creativity, or art or music specifically, please start a separate thread for that, or alternatively explain what Beethoven or (classical) music have to do with "Falsifying Natural Selection". Otherwise your repeated "Beethoven's 9th" questions may start looking like you are trying to distract others from the actual thread topic.

[Ronja]

Sorry guys, this is quite an engaging thread, but now I need to get some sleep. Nighty-night!

[GenesForLife]

This is what you don't understand. The fact that objects have properties is just like a language. According to the American Chemical Society there are some 52 million substances, 50 thousand being added each week, all of them having different properties. In a random universe without intelligence you cannot expect objects to coordinate their properties, no more that you can expect randomness to coordinate a set of 26 letters to form words. mRNA, U, tRNA and ribosomes as well as the other General Transcription Factors they all have to be present at a specific point in a specific time. Basically what it comes down to is

if
mRNA and TRNA and U and Ribosomes
then
cell replication

albeit it is much more complicated than that.

Modern cell replication, lipid bilayers containing self replicating polymers and some external shaking can carry out cell replication, albeit simple.
When will you stop asserting that all protocells were modern cells? or supply evidence that they were?

Just to give you an idea of how hard it is for randomness to coordinate between even very small finite sets, let's imagine that there were only 120 substances in our universe and at one point in time in order to solve a problem only two substance were needed but they needed to be in the right order, even though this series is only two long. That's 120^120, which comes to 10^258 possibilities. To put that in perspective, there are 10^80 atoms, 10^26 nanoseconds in our universe and if we lived in a multiverse where there are as many universes as there are stars in our Universe that would be 10^22, which brings that to a sum total of 10^128. So even if every atom in our universe tried to utter the correct two word combination every nanosecond in every universe in our hypothetical multiverse, the odds of them hitting on the right combination would still one in 10^130.

Complex =/= improbable. The fact that RNA can form spontaneously in water has already been covered in another thread, and to the point of self replication at that.
Try every atom trying to "utter" the right word millions of times and see what the probability is. What you are committing is the serial trials fallacy.

Time to deploy the Blue Butterfly's knowledge of probability on this, when dealing with odds.

Frequently Occurring Fallacies No. 1

A number of fallacies are in circulation amongst the enthusiasts for reality denial, and one that I wish to highlight here is known in scientific circles as "The Error of the One True Sequence". This fallacy asserts that one, and ONLY one, DNA sequence can code for a protein that performs a specific task. This is usually erected alongside assorted bogus "probability" calculations that purport to demonstrate that evolutionary processes cannot achieve what they plainly do achieve in the real world, but those other probability fallacies will be the subject of other posts. Here I want to destroy the myth that one, and ONLY one, sequence can ever work in a given situation.

Insulin provides an excellent example for my purposes, because insulin is critical to the health and well being of just about every vertebrate organism on the planet. When a vertebrate organism is unable to produce insulin, the well-known condition of diabetes mellitus, then the ability to regulate blood sugar is seriously disrupted, and in the case of Type 1 diabetes mellitus, in which the beta-cells of the Islets of Langerhans in the pancreas are destroyed by an autoimmune reaction, the result is likely to be fatal in the medium to long term due to diabetic nephropathy resulting in renal failure.

Consequently, the insulin molecule is critical to healthy functioning of vertebrate animals. The gene that codes for insulin is well known, and has been mapped in a multiplicity of organisms, including organisms whose entire genomes have been sequenced, ranging from the pufferfish Tetraodon nigroviridis through to Homo sapiens. There is demonstrable variability in insulin molecules (and the genes coding for them) across the entire panoply of vertebrate taxa. Bovine insulin, for example, is not identical to human insulin. I refer everyone to the following gene sequences, all of which have been obtained from publicly searchable online gene databases:

[1] Human insulin gene on Chromosome 11, which is as follows:

atg gcc ctg tgg atg cgc ctc ctg ccc ctg ctg gcg ctg ctg gcc ctc tgg gga cct gac
cca gcc gca gcc ttt gtg aac caa cac ctg tgc ggc tca cac ctg gtg gaa gct ctc tac
cta gtg tgc ggg gaa cga ggc ttc ttc tac aca ccc aag acc cgc cgg gag gca gag gac
ctg cag gtg ggg cag gtg gag ctg ggc ggg ggc cct ggt gca ggc agc ctg cag ccc ttg
gcc ctg gag ggg tcc ctg cag aag cgt ggc att gtg gaa caa tgc tgt acc agc atc tgc
tcc ctc tac cag ctg gag aac tac tgc aac tag

which codes for the following protein sequence (using the standard single letter mnemonics for individual amino acids, which I have colour coded to match the colour coding in this diagram of the insulin synthesis pathway in humans):

MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKT
RREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKR
GIVEQCCTSICSLYQLENYCN

Now, I refer everyone to this data, which is the coding sequence for insulin in the Lowland Gorilla (differences are highlighted in boldface):

atg gcc ctg tgg atg cgc ctc ctg ccc ctg ctg gcg ctg ctg gcc ctc tgg gga cct gac
cca gcc gcg gcc ttt gtg aac caa cac ctg tgc ggc tcc cac ctg gtg gaa gct ctc tac
cta gtg tgc ggg gaa cga ggc ttc ttc tac aca ccc aag acc cgc cgg gag gca gag gac
ctg cag gtg ggg cag gtg gag ctg ggc ggg ggc cct ggt gca ggc agc ctg cag ccc ttg
gcc ctg gag ggg tcc ctg cag aag cgt ggc atc gtg gaa cag tgc tgt acc agc atc tgc
tcc ctc tac cag ctg gag aac tac tgc aac tag

this codes for the protein sequence:

MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKT
RREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKR
GIVEQCCTSICSLYQLENYCN

which so happens to be the same precursor protein. However, Gorillas are closely related to humans. Let's move a little further away, to the domestic cow, Bos taurus (whose sequence is found here):

atg gcc ctg tgg aca cgc ctg cgg ccc ctg ctg gcc ctg ctg gcg ctc tgg ccc ccc ccc
ccg gcc cgc gcc ttc gtc aac cag cat ctg tgt ggc tcc cac ctg gtg gag gcg ctg tac
ctg gtg tgc gga gag cgc ggc ttc ttc tac acg ccc aag gcc cgc cgg gag gtg gag ggc
ccg cag gtg ggg gcg ctg gag ctg gcc gga ggc ccg ggc gcg ggc ggc ctg gag ggg ccc
ccg cag aag cgt ggc atc gtg gag cag tgc tgt gcc agc gtc tgc tcg ctc tac cag ctg
gag aac tac tgt aac tag

Already this is a smaller sequence - 318 codons instead of 333 - so we KNOW we're going to get a different insulin molecule with this species ... which is as follows:

MALWTRLRPLLALLALWPPPPARAFVNQHLCGSHLVEALYLVCGERGFFYTPK
ARREVEGPQVGALELAGGPGAGGLEGPPQKRGIVE
QCCASVCSLYQLENYCN

clearly a different protein, but one which still functions as an insulin precursor and results in a mature insulin molecule in cows, one which differs in exact sequence from that in humans. Indeed, prior to the advent of transgenic bacteria, into which human insulin genes had been transplanted for the purpose of harnessing those bacteria to produce human insulin for medical use, bovine insulin harvested from the pancreases of slaughtered beef cows was used to treat diabetes mellitus in humans. Now, of course, with the advent of transgenically manufactured true human insulin, from a sterile source, bovine insulin is no longer needed, much to the relief of those who are aware of the risk from BSE.

Moving on again, we have a different coding sequence from the tropical Zebrafish, Danio rerio, (sequence to be found here) which is as follows:

atg gca gtg tgg ctt cag gct ggt gct ctg ttg gtc ctg ttg gtc gtg tcc agt gta agc
act aac cca ggc aca ccg cag cac ctg tgt gga tct cat ctg gtc gat gcc ctt tat ctg
gtc tgt ggc cca aca ggc ttc ttc tac aac ccc aag aga gac gtt gag ccc ctt ctg ggt
ttc ctt cct cct aaa tct gcc cag gaa act gag gtg gct gac ttt gca ttt aaa gat cat
gcc gag ctg ata agg aag aga ggc att gta gag cag tgc tgc cac aaa ccc tgc agc atc
ttt gag ctg cag aac tac tgt aac tga

And this sequence codes for the following protein:

MAVWLQAGALLVLLVVSSVSTNPGTPQHLCGSHLVDALYLVCGPTFTGFFYNP
KRDVEPLLGFLPPKSAQETEVADFAFKDHAELIRK
RGIVEQCCHKPCSIFELQNYCN

so again we have a different insulin precursor protein that is ultimately converted into a different insulin molecule within the Zebra Fish.

I could go on and extract more sequences, but I think the point has already been established, namely that there are a multiplicity of possible insulin molecules in existence, and consequently, the idea that there can only be ONE sequence for a functional protein, even one as critically important to life as insulin, is DEAD FLAT WRONG. Now, if this is true for a protein as crucial to the functioning of vertebrate life as insulin, you can be sure that the same applies to other proteins, including various enzymes, and therefore, whenever the "One True Sequence" fallacy rears its ugly head in various places, the above provides the refutation thereof.


Frequently Occurring Fallacies No. 2

For the second of the fallacies that tends to appear in reality-denial attempts to dismiss the validity of evolution, I have decided to cover the Serial Trials Fallacy. This usually, but not always, accompanies the One True Sequence fallacy above. However, the nature of this fallacy arises via an entirely different mechanism.

Typically, what happens is that a probability calculation is constructed, usually on the basis of assumptions that are either left unstated altogether (conveniently preventing independent verification of their validity), or if they are stated, they usually fail to survive intense critical scrutiny. However, even if we allow these assumptions to remain unchallenged, the appearance of the Serial Trials fallacy means that destruction of the validity of the spurious probability calculation is easy even without resorting to the effort of destroying those other assumptions.

Basically, the Serial Trials Fallacy consists of assuming that only one participant in an interacting system is performing the necessary task at any one time. While this may be true for a lone experimenter engaged in a coin tossing exercise, this is assuredly NOT true of any system involving chemical reactions, which involves untold billions of atoms or molecules at any given moment. This of course has import for abiogenesis as well, against which bad probability calculations and the Serial Trials Fallacy are routinely deployed. I shall concentrate here on abiogenetic scenarios, but what follows applies equally to nuclear DNA replication and any absurd arguments based upon bad probability calculations and the Serial Trials Fallacy that mutations cannot occur in a given amount of time.

The idea is simply this. If you only have one participant in the system in question, and the probability of the desired outcome is small, then it will take a long time for that outcome to appear among the other outcomes. But, if you have billions of participants in the system in question, all acting simultaneously, then even a low-probability outcome will occur a lot more quickly.

For example, if I perform trials that consist of ten coin tosses in a row per trial, and this takes about 20 seconds, then I'm going to take a long time to arrive at 10 heads in a row, because the probability is indeed 1/(210) = 1/1024. In accordance with a basic law of probability, namely that if the probability of the event is P, the number of serial trials required will be 1/P, I shall need to conduct 1,024 serial trials to obtain 10 heads in a row (averaged over the long term of course) and at 1 trial every 20 seconds, this will take me about six hours, if all I do is toss coins without any breaks for sleep, food or other necessary biological functions. If, however, I co-opt 1,024 people to perform these trials in parallel, at least one of them should arrive at 10 heads from the very outset. If I manage by some logistical wonder to co-opt the entire population of China to toss coins in this fashion, then with a billion people tossing the coins, we should see 1,000,000,000/1024, which gives us 976,562 Chinese coin tossers who should see 10 heads in a row out of the total 1,000,000,000 Chinese.

Now given that the number of molecules in any given reaction even in relatively dilute solutions is large (a 1 molar solution contains 6.023 × 1023 particles of interest per litre of solution, be they atoms, molecules or whatever) then we have scope for some serious participating numbers in terms of parallel trials. Even if we assume, for the sake of argument in a typical prebiotic scenario, that only the top 100 metres of ocean depth is available for parallel trials of this kind (which is a restriction that may prove to be too restrictive once the requisite experimental data are in from various places around the world with respect to this, and of course totally ignores processes around volcanic black smokers in deep ocean waters that could also fuel abiogenetic reactions) and we further assume that the concentration of substancers of interest is only of the order of millimoles per litre, then that still leaves us with the following calculation:

[1] Mean radius of Earth = 6,371,000 m, and 100 m down, that radius is 6,370,900 m

[2] Volume of sea water of interest is therefore 4/3π(R3-r3)

which equals 5.1005 × 1016 m3

1 litre of solution of 1 mmol l-1 will contain 6.023 × 1020 reacting particles of interest, which means that 1 m3 of solution will contain 6.023 × 1026 particles, and therefore the number of particles in the 100 metre layer of ocean around the world will be 3.0730 × 1043 particles. So already we're well into the territory where our number of parallel trials will make life a little bit easier. At this juncture, if we have this many interacting particles, then any reaction outcome that is computed to have a probability of greater than 1/(3.073 ×1043) is inevitable with the first reaction sequence.

Now, of course, this assumes that the reactions in question are, to use that much abused word by reality denialists, "random" (though their usage of this word tends to be woefully non-rigorous at the best of times). However, chemical reactions are not "random" by any stretch of the imagination (we wouldn't be able to do chemistry if they were!), which means that once we factor that into the picture alongside the fact that a parallel trial involving massive numbers of reacting molecules is taking place, the spurious nature of these probabilistic arguments against evolution rapidly become apparent.

The same parallel trials of course take place in reproducing populations of organisms. Of course, the notion falsely propagated by reality denialists is that we have to wait for one particular organism to develop one particular mutation, and that this is somehow "improbable". Whereas what we really have to wait for is any one organism among untold millions, or even billions, to develop that mutation, for evolution to have something to work with. If that mutation is considered to have a probability of 1/109, then we only have to wait for 109 DNA replications in germ cells to take place before that mutation happens. If our working population of organisms is already comprised of 1 billion individuals (last time I checked, the world human population had exceeded 6.6 billion) then that mutation is inevitable.

So, next time you see a spurious probability calculation appearing that purports to "disprove evolution", look out for two salient features, namely:

[1] Base assumptions that are either not stated altogether (thus conveniently preventing independent verification) or base assumptions that fail to withstand critical scrutiny, and

[2] The Serial Trials Fallacy above.

Sums up where you are going wrong with respect to odds nice and clean.

Edit - in quite a few places superscripts for powers have been lost. Therefore it would make sense to read the original post as well, here at http://forum.richarddawkins.net/viewtop ... =4&t=46882

[GenesForLife]

And I would find it hilarious if someone decided to dismiss Cali as being wrong wrt basic probability, he's after all, from what I know, a mathematics graduate with tensor calculus in his remit.

[Svartalf]

I dismiss Cali, I only need one master science guy, and you fit the bill... anyway, everybody knows Einstein was wrong : god plays dice, loaded ones so he never loses.

[GenesForLife]

You wouldn't want to trust me on mathematics lol. I got a flimsy second class at Pre-Uni college

[spinoza99]

[ q u o t e = " calli " ]


I f t h a t m u t a t i o n i s c o n s i d e r e d t o h a v e a p r o b a b i l i t y o f 1 / 1 0 9 , t h e n w e o n l y h a v e t o w a i t f o r 1 0 9 D N A r e p l i c a t i o n s i n g e r m c e l l s t o t a k e p l a c e b e f o r e t h a t m u t a t i o n h a p p e n s .
[/quote]

I sure would like to know how he got that 1/109 probability.

In any case, regarding the one true sequence. I have already made my position clear on this issue. With 20 Amino Acids that must be sequenced into a protein 120 long, there are 10^150 possible sequences. So even if you say that there are 10^80 possible sequences, which there are not, then the odds are still 1 in 10^70 that you will hit a correct sequence.


As for Calli being a math major, look at Isaac Newton, he wrote more on Biblical commentary than he did on science.

[GenesForLife]

And your assumptions still don't take ribozymal activity into account, ribozymes that make polypeptides and oligonucleotides that do the same can themselves form without external aid from proteins, and these offer a direct example of non-random processes for protein production, how have you accounted for this in your conclusions?

Re: Newton, false analogy much? Newton did not write biblical commentary when doing physics, he did physics and maths when dealing with physics and maths. Newton was also an alchemist, this says anything about Newton's ability as a physicist how exactly?

If you want to ask him how he got that number you could ask by PM.

[GenesForLife]

What is wrong with your quoting, by the way? It looks like someone went poking an elephant's dick into the onscreen space between successive letters in words? or is it just my computer that is displaying messed up quoting?

[Feck]

Issac Newton was a Christian ! woops Canard warning Mendel was a priest ! So what ? Please don't tell us that Hitler and Stalin were atheists or I swear I will wet myself !

[JimC]

What is wrong with your quoting, by the way? It looks like someone went poking an elephant's dick into the onscreen space between successive letters in words? or is it just my computer that is displaying messed up quoting?

Yes, spinoza, please use the correct quote button, it is very distracting as is...