Yeates' research blurs the distinction between eukaryotic cells and those of prokaryotes by showing that bacterial cells are more complex than scientists had imagined.

Based on his teleological thinking, and his hypothesis of front-loaded evolution, Mike Gene has been predicting for years that scientists would eventually find out that bacteria were more than a bag of enzymes, and that the complexity of their inner structure wouldn't be that much simpler than eukaryotes. KUDOS, Mike!!!

AdR: In my definition, phylogenetic evidence would be based on actual gene sequences and molecular biology.

phylo-: tribe : race : phylum {phylogeny}
-geny: generation : production {phylogeny}

The question is the hereditary relationships. You don't have to know the molecular genetic sequence of dinosaurs to determine their hereditary relationships, or the history of their descent.

AdR: I don't reject common descent at all, although I don't know how the transitions in the tree or the bi- or tri- or multi-furcations were caused.

If you don't reject common descent, then look at the diversification of dinosaurs again. You will see that what seems like radical macroevolutionary adaptations when we look at the end-points of transitions is actually stepwise changes over millions of years.

AdR: Exactly, but in order to define specialization and flexibility, you need to think in teleological, engineering terms.

We don't *need* to think in those terms. It is quite possible to model the relationship between specialization, flexibility, and the rate of environmental stress without invoking teleology.

AdR: Exactly, but in order to define specialization and flexibility, you need to think in teleological, engineering terms.

I think most humans are only capable of seeing things like this in "teleologic" terms, but I have no reason to believe this is anything more than a limitation of human thinking. We are highly biased by how we think and its very hard for most people to see beyond those biases to imagine other possibilities.

AdR:TB, if you claim that evolution is non-teleologic by nature, you should refrain from using teleological language. If you cannot explain evolution in non-teleological terms, as seems to be the case, maybe evolution is teleological.

But this is the very thing I disagree with. You cannot claim certain words are your own and mean what you want them to mean regardless of what the speaker wants them to mean. It is the English language which is "teleologic" in its usage patterns, you are effectively suggesting that Science shouldn't be allowed to use English. And it is human nature to personify things and speak of them as active agents, you are effectively suggesting that humans shouldn't be allowed to discuss science using natural language. Biology could easily be discussed in technically accurate ways using "non-teleologic" terminology but to do so would involve creating a complicated jargon that makes the topic harder to understand for us English speaking humans. Instead existing "teleologic" terms are repurposed to support a non-teleological meaning. This doesn't imply that teleologic terminology is required, only that it is easily understood.

In my definition, phylogenetic evidence would be based on actual gene sequences and molecular biology. I don't reject common descent at all, although I don't know how the transitions in the tree or the bi- or tri- or multi-furcations were caused. I think that evolution can indeed go very fast, but I doubt of the RM+NS models will be of any value for our understanding of evolution. To me it is like the fuel of a car: I need it but it doesn't help me a bit in understanding the workings of a car.

I also see the tremendous value of the population as a design pattern for easy change, but we have to wonder if that is not innate to the species, i.e. the species has a built-in hidden variety that can be exposed when challenged. Maybe a large part of the driving force of evolution comes from real survival, i.e. after a catastrophic evens. But quickly we don't talk about optimized fitness and higher survival rates of advantageous mutations anymore. Instead, we have to talk about rigging the system with fail-safe mechanisms, pre-empting unknown challenges, or fallback systems to earlier working versions (like software).

Extinction is an important evolutionary process. There are tradeoffs between specialization and flexibility.

Exactly, but in order to define specialization and flexibility, you need to think in teleological, engineering terms.

AdR: Any deviations to an optimized/adapted function will cause diminished survival/fitness.

Zachriel: Ah, there's your problem. You need to get outside more. If you actually observe organisms, they often exhibit a great deal of diversity in traits.

Generally speaking I agree with AdR. The key word is optimized. I can recall at least one instance where a decrease in functionality enhanced fitness in a prokaryotic organism but the enhanced fitness was localized and particular to a specific problem. Elimination of the environmental challenge witnessed a return to prior allele frequency. Diversity can of course arise over time but I suspect it does not usually come at the cost of decreasing a vital function.

AdR: But that's not how evolution works. It is supposed to be a slow gradual process…

We can actually measure the rate of evolution (e.g. in darwins). And it can be very rapid; much more rapid than required to explain the historical record.

AdR: … whereas environmental changes can be very quick.

Yes, they can. That's why genetic diversity is important to a robust population. And a varied population can evolve quickly, especially with sexual selection acting as an amplifier. We can actually observe evolution on this scale.

AdR: Any deviations to an optimized/adapted function will cause diminished survival/fitness.

Ah, there's your problem. You need to get outside more. If you actually observe organisms, you will find that they often exhibit a great deal of diversity in traits.

Consider a great scientist, such as Charles Darwin. His historic voyage around the world included detailed observations of many different organisms. His subsequent scientific output made him one of the greatest scientist of the age"”not even considering his Theory of Evolution.

AdR: We see that even minute changes in environment can wipe out entire species.

Sometimes. Sometimes not. Pandas and Gorillas seem very limited in their ecological flexibility. Cockroaches and mice can rapidly adapt to many different environments. Birds just migrate to greener climes.

Extinction is an important evolutionary process. There are tradeoffs between specialization and flexibility.

To me it seems that organisms have strived to maintain their environment at all costs.

There's that teleological "strived". And what do you mean by "at all costs"

We see that even minute changes in environment can wipe out entire species. It's extinction we observe more than evolution in response to environmental challenges.

Both extinctions and evolution/adaptation are observed as a result of environmental change. What makes you think extinction occurs more often?

You are right about decreases in complexity. I think the bacterial/prokaryote line is an example.

Interesting idea. Why do you think so?

AdR: I make a distinction between evolution and adaptation, or macro and microevolution. I am interested in macroevolution and as long as we do not know how that works, we don't know how evolution works.

The Pluralis majestatis again. We know quite a lot about how evolution works. A primary mechanism of adaptation is natural selection, but there are a variety of other mechanisms at work.

AdR: I don't contest that evolution happened, but I argue here that we do not understand how it works… I assume that the dinosaur graph is not based on phylogenetic evidence, but on gross anatomical features.

Phylogeny, the evolutionary history of a kind of organism. Of course, it's phylogenetic evidence.

AdR: I don't contest that evolution happened, but I argue here that we do not understand how it works.

Do you reject Common Descent of Dinosauria? If so, then we need to start with that. If not, then the phylogenetic tree provides a important evidence concerning the process of stepwise adaptation.

Raevmo: You are assuming a fixed fitness-landscape, but in fact the fitness-landscape is ever-changing because of the ever-changing environment. Today's peak maybe tomorrow's valley.

But that's not how evolution works. It is supposed to be a slow gradual process, whereas environmental changes can be very quick. Any deviations to an optimized/adapted function will cause diminished survival/fitness. A change in environment will lead to valleys in an adapted individual, and the chance that a changing environment will actual benefit the population is small. I have seen fitness-lanscape pictures where they created a fitness bridge between peaks. But as long as we do not know the real molecular counterparts of the peaks, we don't know how the deep the valleys are.

To me it seems that organisms have strived to maintain their environment at all costs. We see that even minute changes in environment can wipe out entire species. It's extinction we observe more than evolution in response to environmental challenges.

You are right about decreases in complexity. I think the bacterial/prokaryote line is an example.