Potential falsifications of the theory of evolution

All of the DNA sequence changes discussed here are random with respect to fitness just as neo-Darwinism states. The DNA changes elicited by environmental stress are neutral, beneficial, and detrimental with respect to fitness. No, it is not. What would run contra to what I am saying is if specific environmental stresses caused only specific mutations that only resulted in an increase in fitness. This is not what we see. What we see is an increase in transposon integration all over the genome, some of which are beneficial and are selected for.

Sure it is. The problem is that the evidence just isn't there, or it is overplayed as in the case of both Shapiro and Koonin. Based on what evidence?

You have things backwards. What evidence convinced you that Shapiro is right?

I didn't ask for his CV. I asked for the evidence that convinced you. What is it?BTW, my username is Taq (with a Q). It's short for Thermus aquaticus which is the bacterial species famous for it's temperature tolerant DNA polymerase used in PCR (in case you were curious).Edited by Taq, : No reason given.

Mutations are still observed to be random with respect to fitness which is the whole point. The cell does not sense antibiotics in the environment and then specifically mutate a specific gene to produce antibiotic resistance, as one example. Instead, random mutations produce the resistance which is then selected for.Edited by Taq, : No reason given.

I think it may be more productive if we start with the data. Once we all agree on what the data says we can better discuss what Shapiro is really saying.

You are pulling small phrases out of their context. That seems to be the problem.I think we would both agree that humans are self-aware and make decisions. However, humans don't decide which mutations are produced in their gametes and which alleles will be passed on to the next generation. Self-awareness and decision making are separate entities from the process of mutation.

He doesn't "go beyond". He uses a different definition, one that does not impact the Modern Synthesis. The key phrase is here:"These phenomena show us that cells are capable of altering their genomes in non-random but not rigidly specified or pre-determined ways."What Shapiro is talking about is that mutations are non-random with respect to time and sequence. The Modern Synthesis is based on the idea that mutations are random with respect to fitness. Shapiro agrees by saying that these mutations are not "rigidly specified or pre-determined".

So what evidence did Shapiro present in those papers that convinced you he was right?This isn't a suggested reading forum. This is a discussion forum. If you think that Shapiro's findings are important then discuss his findings, including the evidence that Shapiro uses to support his claims. When these experts testify they have to present the evidence that led to their conclusions, do they not?

No one has suggested that HGT is responsible for ALL adaptations. The pathways that you talk about utilize random mutations with respect to fitness. Everything from the SOS mechanism seen in bacteria to the systems that Shapiro talks about increase the random mutation rate during times of stress. It would seem that the "intelligent pathways" utilize random mutation and selection. Epigenetics can not explain the morphological and physiological differences between species. There is no epigenetic pathway that will allow a chimp to give birth to a human. There is no epigenetic pathway that will cause skydivers to grow wings. The differences between species is due to a difference in DNA sequence, not a difference in histone packaging or DNA methylation.

All, some, or none of them. It all depends on the mutation. It also depends on the mixture of mutations that occurred in your parents that are then passed on to you.One thing is for sure. When biologists sit down to figure out why humans and chimps are different the first place they look is at the DNA sequence, not at the differences in DNA methylation or histone packaging (which is the basis for epigenetics). The differences between humans and chimps is due to the different mutations accumulated in each lineage, not a difference in epigenetic changes which only last for a few generations to begin with.Edited by Taq, : No reason given.

To be fair, in order for children to look different than their parents all it takes is a mixture of alleles from mom and dad.

There are mutations caused by physical and chemical processes, such as chemical mutagens or ionizing radiation. These reactions alter the chemical makeup of the DNA resulting in direct changes to the sequence or misreading of the DNA by polymerases (the enzymes that copy DNA during replication).Another source of mutations are changes made by the polymerases themselves due to the inherent properties of the protein. In the following study they found that there is a loose fit between the polymerase and incoming nucleotides that are used to copy the DNA.

quote:

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Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15803-8. Epub 2005 Oct 25.

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Probing the active site tightness of DNA polymerase in subangstrom increments.
Kim TW, Delaney JC, Essigmann JM, Kool ET.

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Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.

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Abstract
We describe the use of a series of gradually expanded thymine nucleobase analogs in probing steric effects in DNA polymerase efficiency and fidelity. In these nonpolar compounds, the base size was increased incrementally over a 1.0-A range by use of variably sized atoms (H, F, Cl, Br, and I) to replace the oxygen molecules of thymine. Kinetics studies with DNA Pol I (Klenow fragment, exonuclease-deficient) in vitro showed that replication efficiency opposite adenine increased through the series, reaching a peak at the chlorinated compound. Efficiency then dropped markedly as a steric tightness limit was apparently reached. Importantly, fidelity also followed this trend, with the fidelity maximum at dichlorotoluene, the largest compound that fits without apparent repulsion. The fidelity at this point approached that of wild-type thymine. Surprisingly, the maximum fidelity and efficiency was found at a base pair size significantly larger than the natural size. Parallel bypass and mutagenesis experiments were then carried out in vivo with a bacterial assay for replication. The cellular results were virtually the same as those seen in solution. The results provide direct evidence for the importance of a tight steric fit on DNA replication fidelity. In addition, the results suggest that even high-fidelity replicative enzymes have more steric room than necessary, possibly to allow for an evolutionarily advantageous mutation rate.
Probing the active site tightness of DNA polymerase in subangstrom increments - PMC

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Effeciency refers to the speed at which the reactions occur and fidelity refers to the accuracy of the polymerases. They found that there is a loose fit between the polyermase and the chemicals it is interacting with resulting in the wrong base being inserted once in a long while.As you can see, this is not tied to fitness. Environmental pressures can not cause a mutation at a specific base in a specific gene. Even when PCR amplifying a single gene with the same sequence over and over there are mutations at different spots.

Let's use heliocentrism as an analogy. Is there any evidence that would falsify the theory that the Earth orbits the Sun? Outside of a Matrix-type universe where we are being fed falsehoods, I really can't think of any evidence that would topple this theory.However, there is some hotshot geocentrist that thinks he has found a chink in the armor. He found a quote from Galileo himself that spoke about the circular orbit of the Earth. HELIOCENTRISM IS NOW FALSIFIED!!!! Why, you ask? Earth follows an elliptical orbit, not a circular one. Heliocentrism is now falsified, right?Sorry, meant to include this in the original post: Of the genetic differences between humans and chimps, which could not be produced by the process of random mutation? Perhaps we should start here.Edited by Taq, : No reason given.

As RAZD mentions, this is somewhat arbitrary. It's like asking when someone stops being a child and becomes an adult. We can't pick a specific nanosecond when this occurs without being arbitrary even if the differences between a 10 year old and 30 year old are obvious to everyone. The same applies to changes in species through time. At the ends of the spectrum the differences are very obvious, but it is impossible to pick the single generation in which they moved from being one species to the next.