Calculating the odds of life

[GenesForLife]

Genes,

you are not an objective scientist because you've clearly expressed an extreme repugnance for any ideas which imply intelligent design. you will always bend the results of your findings to please you. you will ignore evidence that refutes your cherished beliefs, and you will focus on evidence that confirms it. an ethical scientist has no emotional interest in any one theory, the only thing that matters is the truth and he accepts whatever that truth is without emotion. you clearly have an emotional investment in atheism as demonstrated by your numerous insults. you wouldn't use insults in a phd thesis, so why do you use them now?

Arugmentum ad hominem much? Your argument doesn't stand up to scrutiny, and that is all that matters, "you have an emotional investment therefore my argument is not flawed" is a nonsensical statement. Atheism is a lack of belief, and the default position, philosophically or otherwise, puts the burden of proof on you. Regarding PhD theses, the work involved therein is based on subjects and a body of literature that is evidentially supported (in other words, anything other than ex-recto blind assertions), which doesn't apply to your argument because they are strawmen, come again. I find errant nonsense repungant, whether that be lamarckism or faulty arguments, next. Also, blatant case of projection much?

You have pointed to flaws in my calculation of the odds without you yourself offering odds based on your own calculations. I already demonstrated that even if we assume that all life came from a creature which was half as complex Mycoplasma Mycoides, the odds would still be one in 900 googols. There has be to some threshold in which life is not possible with a particular DNA sequence. You cannot sequence DNA anyway you like and expect it to replicate. A true, good and virtuous atheist does not believe in anything without evidence, so believing that life came from a being of one fifth the complexity of the Mycoplasma Mycoides would be to commit the cardinal sin of atheism: to believe in something for which there is no evidence. Humans share 90% of their DNA with a tree. All advanced life has 90% of the DNA in common. Therefore it is rational that 90% of the DNA found in the Mycoplasma Mycoides must be sequenced in an exact way, but even if we assume that only 25% of it need be sequenced in an exact way then the odds are still one in 450 googols that it could be sequences at random.

1) An argument doesn't become valid despite flaws because opponents don't put provide an alternative (say for instance you are in a court defending someone who has been wrongly accused, proving his innocence does not require that you find the real culprit, so here your argument is not logically valid.

2) I'd like to see citations for the 90% of all higher organisms sharing complex DNA, and you missed my point about any possible sequence being capable of being produced from chemical processes acting on precursor sequences, and that treshold for self replicability isn't anything like a Mycoplasma mycoides genome. So, your assertion that it is "rational" is nonsense.

The fundamental laws of genetics allow the inheritance and the expression of a vast majority of alleles independent of sequence or the order in which they're present on a genome, I will be waiting for evidence that 90% of the genomes of all higher organisms is in the same sequence, good luck finding it, that stat very probably applies to orthologous proteins, that the same proteins doing the same function in both trees and humans may have a 90% similarity in cases of specific proteins, you can just go to Genbank, retrieve sequences for a protein, run a similarity search and look at how much variation there can be from the query sequence and related sequences, this alone is enough to render your strawman false, the argumentum ad hominem in the first paragraph.

In any case, the onus is on you to back your assertion that whole genomes (not protein coding exons in orthologous sequences) have to be sequence specific to be functional and to an extent of 90%, I'll not be holding my breath.

I gave the atheists an enormous benefit of the doubt in assuming that the number of events at our disposal is roughly a max of 2 googols, in reality it is probably closer to .3 googols, if not .1 googols. I assumed that the max number of events was equal to the number of atoms in the universe linking with one another each billionth of a second that has existed in our universe's history, moreover i assumed that there are as many Universes in existence as there are atoms in the Universe.

Much appreciated, still doesn't confer any validity to your argument.

In reality, to be honest we would have to divide the number of nitrogen atoms in our universe by however many it takes to make one DNA base pair and it's about 20 or so, then we have to restrict the time to the time after the first galaxies arose.

And we cannot stop there. If we wanted we could try to calculate the odds of the Cambrian Explosion, an extraordinarily unlikely event probably equal to one in a million googols.

Interesting, what do you know of the Cambrian Explosion? (If you are going to assert that species appeared then out of nowhere expect to have evidence to the contrary handed to you on a platter, since I do already have links to several papers describing Precambrian fossils, also note that the fossilisability of organisms or the lack thereof doesn't rule out the presence of organisms, and it is a known fact that soft bodied animals do not necessarily fossilise well at all, in any case, the Ediacaran fauna is enough to refute any attempts to prop up assertions about the caricatured version of the Cambrian explosion (which, by the way, lasted 23 million years or so by some of the more popular estimates)

You also conveniently ignored the question: how does randomness select the correct properties from an infinite set of properties. In our Universe, F = MA,
all three of those letters are properties. Randomness has no ability to make properties work in coordination with each other. Randomness can only select the right answer from a finite list some of the time, randomness cannot do what humans do every day: the amount of utterances at a human's disposal is infinite, and yet we utter grammatically correct utterances about 99% of the time. If you randomness is instructed to produce from an infinite list a correct formulation such as F = MA it will never accomplish the task. If the odds that will fail are one in an infinity, then you will always fail.

Testable, well defined natural processes are NOT random, way to miss the flippin' point.

Another poster offered the possibility that there are infinite universes. This is committing the cardinal sin of atheism which is to believe in something for which there is no evidence.

This is actually the more parsimonious explanation when dealing with the possibility of multiple quantum inflations, since you will have to assume a barrier to preventing other "universes" from forming otherwise. There is no cardinal sin of atheism because atheism is NOT a doctrine, category error much?

Chemical processes are random in that you cannot predict, in a mixture of reagents, which particular reagent molecules will react and which won't, but the process of bonding is NOT.

True, the process of bonding is not random. Bonding is a property. Randomness cannot choose the correct properties such that several properties will coordinate to form something like life. Even if that were true, that randomness could select properties, randomness cannot sequence material into a correct sequence of which the odds are one in 100 googols if only a half of a googol of events is at its disposal.

I have explained why this (sequence thing) is a strawman, and I expect you to handwave this away again, just go look at Genbank, gene maps, and locus mapping, and also find out where in the scientific literature it is postulated that all life evolved from Mycoplasma mycoides genomes,and that it is the minimally required component for all life and also the asinine idea that whole genome sequences have to be conserved and necessary, the fact that we have the flagellum, which is purportedly irreducibly complex, capable of evolving from a Type 3 Secretory system through the Mullerian Two Step of adding a part and making it necessary by selection, since the dynamics of multicomponent systems is altered by the addition of the new component, to the point that the component in question becomes integral is enough to suggest that your strawman is, well, a strawman.

So, to sum up, you persist with a strawman, several dodgy pieces of logical reasoning, and an argumentum ad hominem which is the cherry on the cake, all the while offering unsubstantiated, uncited assertions, and yet you demand that your argument is something that must be treated with the same respect that evidentially supported stuff gets when being dealt with as part of a PhD thesis? The reason insults are not used in a PhD thesis is because the work being dealt with doesn't call for it, this does, now get over it.

[Gawdzilla Sama]

IBH, life never actually occurred. I'm just imagining you lot.

[PsychoSerenity]

Wooo! Go Genes!

Is spinoza for real or just trollin'? I never can tell.

Either way, it would be nice to see a genuine "odds of life", given the starting conditions of an early earth, and our best models of chemical evolution etc., over a time period of a few billion years.

Twenty-two amino acids were created, in a small flask, in a week, in the Miller–Urey experiment - so I'm guessing the odds are higher than the "impossible" that spinoza is talking about.

[GenesForLife]

And oh, the 90% of all higher organisms assertion is a bare faced lie, not least because we haven't sequenced 90% of higher organisms that are extant today, let alone 90% of all higher organisms to have ever lived, care to present something that is a bit closer to the truth, next time round? And you so conveniently ignored that the fundamental requirement for self-replication is nowhere near what is required for a fully functional Mycoplasma mycoides genome.

Just to bolster that point,

A self-replicating molecule directs the covalent assembly of component molecules to form a product that is of identical composition to the parent. When the newly formed product also is able to direct the assembly of product molecules, the self-replicating system can be termed autocatalytic. A self-replicating system was developed based on a ribozyme that catalyzes the assembly of additional copies of itself through an RNA-catalyzed RNA ligation reaction. The R3C ligase ribozyme was redesigned so that it would ligate two substrates to generate an exact copy of itself, which then would behave in a similar manner. This self-replicating system depends on the catalytic nature of the RNA for the generation of copies. A linear dependence was observed between the initial rate of formation of new copies and the starting concentration of ribozyme, consistent with exponential growth. The autocatalytic rate constant was 0.011 min−1, whereas the initial rate of reaction in the absence of pre-existing ribozyme was only 3.3 × 10−11 M⋅min−1. Exponential growth was limited, however, because newly formed ribozyme molecules had greater difficulty forming a productive complex with the two substrates. Further optimization of the system may lead to the sustained exponential growth of ribozymes that undergo self-replication.

http://www.pnas.org/content/99/20/12733.abstract

The sequences involved in that (for self replication) were 5′-pppGAGACCGCAAUCC-3′ and 5′-GGAUUGUGCUCGAUUGUUCGUAAGAACAGUUUGAAUGGGUUGAAUAUA-3′

Fancy 6 million base pairs as being required for the fundamental origins of a self replicating system, there also is no indication that this is the bare minimum required for self replication either.

Just to bring in some scientific literature on this issue...

A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation-based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered.

http://rnajournal.cshlp.org/content/15/5/743.abstract

Clearly the scientific community, which includes theists, before you go crying bias, thinks that a naturalistic origin of the basic, fundamental properties of living organisms is not a problem, in terms of probability or otherwise, so I suggest you dispose your asinine argument.

And oh look, the piece de resistance of my literature search today...

The synthesis of RNA chains from 3′,5′-cAMP and 3′,5′-cGMP was observed. The RNA chains formed in water, at moderate temperatures (40–90 °C), in the absence of enzymes or inorganic catalysts. As determined by RNase analyses, the bonds formed were canonical 3′,5′-phosphodiester bonds. The polymerizations are based on two reactions not previously described: 1) oligomerization of 3′, 5′-cGMP to ∼25-nucleotide-long RNA molecules, and of 3′,5′-cAMP to 4- to 8-nucleotide-long molecules. Oligonucleotide A molecules were further extended by reciprocal terminal ligation to yield RNA molecules up to >120 nucleotides long and 2) chain extension by terminal ligation of newly polymerized products of 3′,5′-cGMP on preformed oligonucleotides. The enzyme- and template-independent synthesis of long oligomers in water from prebiotically affordable precursors approaches the concept of spontaneous generation of (pre)genetic information.

Full paper at http://www.jbc.org/content/284/48/33206.abstract

I counted 50 in the longer of the two ribozymes, why you think that a self replicating system is too improbable to happen without a supernatural entity manually putting things in place is beyond me.

[GenesForLife]

Base transtions by alkylation allow the conversion of one base already in a polymer or otherwise, so deterministic chemistry acting stochastically on polymers formed by the mechanism documented above can produce the sequences required for self replication, no magic required.

[GenesForLife]

I will continue to insist that you provide citations for your sources before even considering your next reply.

[GenesForLife]

More work on the subject...

Our current understanding of biology suggests that early life relied predominantly on RNA for catalysis and replication. Here, we report the isolation of an RNA polymerase ribozyme called B6.61 that exhibits superior extension and fidelity relative to its progenitor, the Round-18 polymerase. The B6.61 polymerase was selected from a mutagenized pool containing ∼ 9 × 1014 sequence variants through the use of a novel large-scale in vitro compartmentalization system. B6.61 polymerized all tested primer–template (PT) complexes faster than the Round-18 variant. For one PT, B6.61 exhibited dramatically faster elongation past one full helical turn and incorporated at least 20 nucleotides of sequence, setting a new extension record for an RNA polymerase ribozyme. The increased efficiency of the B6.61 construct was related to improvements in fidelity, with the new variant incorporating less incorrect wobble base pairs than its parent. This new polymerase demonstrates the feasibility of evolving an artificial RNA replicase ribozyme in the foreseeable future.

These people highlight a ribozyme with RNA polymerase activity. http://rnajournal.cshlp.org/content/13/7/1017.full

Going back to 1993, we have this

Isolation of new ribozymes from a large pool of random sequences
DP Bartel and JW Szostak

Department of Molecular Biology, Massachusetts General Hospital, Boston 02114.

An iterative in vitro selection procedure was used to isolate a new class of catalytic RNAs (ribozymes) from a large pool of random-sequence RNA molecules. These ribozymes ligate two RNA molecules that are aligned on a template by catalyzing the attack of a 3'-hydroxyl on an adjacent 5'-triphosphate--a reaction similar to that employed by the familiar protein enzymes that synthesize RNA. The corresponding uncatalyzed reaction also yields a 3',5'-phosphodiester bond. In vitro evolution of the population of new ribozymes led to improvement of the average ligation activity and the emergence of ribozymes with reaction rates 7 million times faster than the uncatalyzed reaction rate

http://www.sciencemag.org/cgi/content/a ... f_ipsecsha

Basically, what I am saying is that while we do not have the exact mechanism of abiogenesis figured out yet, we have evidence, and are acquiring more and more, demonstrating that the fundamental chemistry of life processes can have naturalistic origins, the evidence is in favour of a naturalistic explanation, and that is the rational position to take, other than witholding opinion, at this point.

[GenesForLife]

peptide bond formation by ribozymal action has also been documented

An attractive solution to the problem of the origin of protein synthesis in an evolving 'RNA world' involves catalysis by nucleic acid without assistance from proteins1,2. Indeed, even the modern ribosome has been considered to be fundamentally an RNA machine3, and the large ribosomal subunit can carry out peptidyl transfer in the absence of most of its protein subunits4. Successive cycles of in vitro selection and amplification5, 6, 7 have been used to find RNAs that perform many biochemical reactions8, 9, 10, 11, 12, 13, 14, 15, 16, including transfer of an RNA-linked amino acid to their own 5'-amino-modified terminus15. Here we demonstrate the in vitro selection of ribozymes (196 nucleotides) that perform the same peptidyl transferase reaction as the ribosome: that is, they can join amino acids by a peptide bond. Like ribosome substrates, one amino acid (N-blocked methionine) is esterified to the 3'(2')-O of adenosine, whereas the acceptor amino acid (phenylalanine) has a free amino group. Our best characterized ribozyme recognizes the amino-acid ester substrate by binding its adenosine moiety, and is therefore capable of utilizing Leu- and Phe- as well as Met-derived substrates. Such lack of specificity with respect to the amino acid is a feature necessary for a generalized protein-synthesizing enzyme.

http://www.nature.com/nature/journal/v3 ... 096a0.html

[Bella Fortuna]

Genes - I understand none of it but your thoroughness and desire to look at evidence is

[GenesForLife]

Very much a future professional requirement, Bella, Cancer Biology is getting madder by the day and when I start Masters' next fall I need to ask questions regarding extant ideas to gain useful insight. If Spinoza or whoever brought up proper peer reviewed citations from reputed journals with high standards of rigour, I'd accept it if warranted, but to calculate odds a priori and make fallacious assumptions about what is actually postulated to have happened leading to the origin of life to set strawmen up gets on my nerve, it's almost as bad as homeopaths saying "Conventional medicine doesn't always work, therefore homeopathy does"

Further questions, Spinoza - define a metric for design. (we associate certain things with being designed since we have evidence of humans engaged in the process of designing and making things) , since you have offered no evidence of any designer at all, let alone address the origins of said designer and its attributes, your argument is a total non-starter, especially in the absence of a metric for design.

Chance or Design is a false dichotomy, natural bottom up processes are also a candidate, and therefore your probability argument falls flat, this apart to all the flaws I've already pointed out in your assumptions about genome sizes.

[Coito ergo sum]

Since we are here, maybe the odds for life were 100%.

[GenesForLife]

That point was already made, Coito, and Spinoza continues to ignore it, probabilities have to be 1 for a priori events, since what could have happened did happen.

[GenesForLife]

I committed a little error there, we're talking of the assertions wrt 90% of the genome being conserved, including genomic sequence, in all extant higher organisms, not 90% of higher organisms having the same DNA , just thought I'd mention this because it would be unfair not to, and I would otherwise end up critiquing what s/he did not say, but once you go to all higher organisms the argument is in even more hot water, reason being we haven't sequenced even a substantial minority of the extant higher organisms, let alone extinct ones.

[GenesForLife]

Just thought I'd post a little list of work on the Precambrian fossil record.


http://www2.nau.edu/~bio222-c/Reserve%2 ... l_1997.pdf
This details a late precambrian bilaterian mollusc called Kimberella.

http://www.sciencemag.org/cgi/content/long/147/3658/563
This bears out the fact that we have known of precambrian fossils for a long long time, and also that their existence has been denied for an equally long time by mythology fetishists

http://palaeontology.palass-pubs.org/pd ... 99-628.pdf
This paper details a rich collection of fossils from Ediacara in South Australia, and was published in 1969. So I suspect those putting up the cambrian explosion canard haven't read anything that dates back to a time after 1969.

From this http://www.sciencedirect.com/science?_o ... b10bd86ddd

we have the following abstract.

The evolutionary divergence of cnidarian and bilaterian lineages from their remote metazoan ancestor occurred at an unknown depth in time before the Cambrian, since crown group representatives of each are found in Lower Cambrian fossil assemblages. We report here a variety of putative embryonic, larval, and adult microfossils deriving from Precambrian phosphorite deposits of Southwest China, which may predate the Cambrian radiation by 25–45 million years. These are most probably of cnidarian affinity. Large numbers of fossilized early planula-like larvae were observed under the microscope in sections. Though several forms are represented, the majority display remarkable conformity, which is inconsistent with the alternative that they are artifactual mineral inclusions. Some of these fossils are preserved in such high resolution that individual cells can be discerned. We confirm in detail an earlier report of the presence in the same deposits of tabulates, an extinct crown group anthozoan form. Other sections reveal structures that most closely resemble sections of basal modern corals. A large number of fossils similar to modern hydrozoan gastrulae were also observed. These again displayed great morphological consistency. Though only a single example is available, a microscopic animal remarkably similar to a modern adult hydrozoan is also presented. Taken together, the new observations reported in this paper indicate the existence of a diverse and already differentiated cnidarian fauna, long before the Cambrian evolutionary event. It follows that at least stem group bilaterians must also have been present at this time.

And by the way, here is a search listing for papers that are relevant to the Precambrian fossil record and the generation of organismal lineages, for those so inclined.

Edit- direct link not working, so I'm going to paste links to relevant freely accessible research papers one after one. (Edit- it appears I may have to put the links into another post, maximum allowed number of URLs is 5)

So, Spinoza, if you are going to assert that at the outset of the cambrian fully formed phyla sprung out of thin air instantaneously by abiogenesis I suggest you drop it, both Metazoan lineages, namely the Bilateria and Cnidaria, were already established millions of years before the cambrian, for which there is evidence as those papers will testify.

[GenesForLife]

Those links...

http://www.ncbi.nlm.nih.gov/pubmed/20009270
http://www.ncbi.nlm.nih.gov/pubmed/19858483
http://www.ncbi.nlm.nih.gov/pubmed/18192188
http://www.ncbi.nlm.nih.gov/pubmed/18192178
http://www.ncbi.nlm.nih.gov/pubmed/16778054