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Permalink Reply by Loop Johnny on November 20, 2010 at 3:38pm

For example, I would like an online up-to-date phylogenetic tree with the discovered species, if it exists.

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Permalink Reply by Loop Johnny on November 20, 2010 at 4:00pm

Appreciate.

I will first try to finish evolution101 so I can properly fill some of my gaps.

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Permalink Reply by Dave G on November 20, 2010 at 4:10pm

In addition to Talk Origins, if you want a good overview of evolution, picking up Jerry Coyne's Why Evolution Is True or Richard Dawkins' The Greatest Show On Earth will give you a solid grounding in the evidence for evolution and its mechanisms.

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Permalink Reply by Dave G on November 20, 2010 at 4:16pm

They can be found on torrents in both PDF and RTF formats. A quick google search turned up a couple active torrents for each, and if network tracking is a problem, I'd recommend using Tor to encrypt and disguise your network activities. Plus, you're able to spoof the origin of your connection so that it will look like the files are being requested from another country.

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Permalink Reply by Radu Andreiu on November 20, 2010 at 4:56pm

The teaching of evolution is not banned in the sense of people not being able to read books or teach others about it. Censorship is not that prevalent here. Evolution and its mechanisms just aren't explained in biology class, but they are taught as the reasons why life is as it is. That is still horrible, but not in the sense of biology being a class where we are taught that God created living beings as they are today.

Maybe you understood that from the beginning, but I wanted to put that out there so that there wouldn't be any misunderstanding. We are in a bad situation, but not that bad.

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Permalink Reply by Radu Andreiu on November 20, 2010 at 4:45pm

Do you know how natural selection works? That pretty much applies to anything self-replicating, which transmits its "blueprint" to its offspring with some errors. There is much evidence for natural selection in terrestrial life, but that's not a surprise given that mentioned before. The real surprise would have been if natural selection (inevitably leading to evolution and diversity, in Earth's complex environment) didn't occur. It is mathematically impossible for the most successful features not to prevail. Probabilities play a crucial role in evolution.

Natural selection is the first thing you need to understand about evolution. As I remember you said you knew some programming, I suggest you make a simple genetic algorithm and see how things work. That helped me understand evolution better, given that I come from the same evolution-free educational system, and also gave me the opportunity to make a statement about the importance of evolution. I did that by using my genetic program as the project for my 12th grade Computers Competence attestation and mentioning the said set-back in our educational system.

Getting back to the algorithm, depending on how well or if you know OOP, you can use dedicated objects to represent you virtual creatures, or just some arrays representing their genetic code. Replicate them with some minor modifications and let them do that for a number of generations. If you implement something to track their development, you will see how they'll evolve, meaning they will increase their chances of reproducing, 'cause that's all there is to natural selection. You can play with the environment: change it a little, or even a lot, and see how mass extinctions suddenly occur.

Understanding the math/logic (not necessarily formal) behind evolution shouldn't let too much to be doubted about its truth. That being said, in the really complex environment that we find ourselves in, there are other natural, and therefore quite evident, mechanisms which drive the modeling of the species. They have much to do with migrations and continents moving around, but they are thoroughly explained in any respected source of information about evolution, so they are quite easy to find. The actual evidence of this has the importance of revealing how much a role each mechanism plays in evolution, what is the path that terrestrial life took and how can we better understand the present and the future with this knowledge.

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Permalink Reply by Greg Gorey on November 20, 2010 at 6:11pm

there was a futurama episode about that recently.

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Permalink Reply by Loop Johnny on November 21, 2010 at 9:02am

I am at the National College of Computer Science Piatra-Neamt and I have thought about the similarities between natural selection ( with it's binary DNA database: A-T, C-G ) and the computer format ( 0 and 1 ).

I know OOP pretty well. Inheritance, patterns, children, parents, properties, methods, polymorphism, all for abstract objects that reside inside a virtual world. I am a Flash website programmer and I am familiar with Object oriented programming. Abstract objects have a tree-like pattern, like the species.

If a self replicating program is created and it receives external stimulus ( input, or environment pressure ) it can change according to how it was programed, by a natural selective method.

Reality is a pretty complex program. The whole factors create a very diverse ecosystem, adapted to the environment in which it lives in.

It all falls in perfectly with the gaps I had. Physics, chemistry, computer science, maths, it completes my image of reality very well. I will continue to explore this field even more.

Also, my biology teacher is not very religious, a tad superstitious, but her teaching methods are very good. She can startle my curiosity. It does not include an evolutionary perspective, but I can complete the version I have inside my mind ( with the functionality of DNA, anatomy, chromosomes, single celled organism functions, etc. ) with evolution. It fills the gaps pretty well.

Thanks T/A for the guidance.

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Permalink Reply by Dark Star on November 22, 2010 at 1:13pm

If you want to explore evolutionary algorithms check out:

http://www.wolframscience.com/

cellular automaton are natural candidates for modeling the physical world:

http://catdir.loc.gov/catdir/samples/cam031/97028284.pdf
http://ebooks.cambridge.org/ebook.jsf?bid=CBO9780511549755
(and many others)

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Permalink Reply by Dark Star on November 20, 2010 at 11:50pm

Resources:
http://www.timetree.org/
http://tolweb.org/tree/

And... http://www.phylointelligence.org/observed.html
The whole site but especially this entry:

When a predator was introduced to the environment of the unicellular Chlorella algae in a lab test, scientists observed the algae cells bond together in colonies, and eventually became an entirely new multicellular species. One could even argue that this change extends past the species level. In the image to the left, FC is the unicellular chlorella algae, Oc is the predator introduced to the environment, and CC is the new multicellular algae.

This is not simply a "cell colony", but a new multicellular organism. The multicellularity was achieved by a mutation that fused the cell wall of the mother cell and its daughter cell together. Because these cells are thus dependent upon each other for survival, the new organism is multicellular and not a simple bacterial colony.(Boraas et al., 1998) (Note: The Image is also from this source.)

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Permalink Reply by Dark Star on November 21, 2010 at 12:28am

Some independent thoughts on evolution:

#1 evolution does NOT attempt to explain the origin of life itself. Although there are many scientific theories in the area of abiogenesis but the simple and direct answer to this question is that we do not know for certain yet. But, at the same time, there is a lot of very promising research into the question and many breakthroughs have been made. For one example, see Dr. Jack Szostak's work and then research from there.

And some examples of failed predictions from Intelligent Design:

* Irreducible complexity of the bacterial flagellum (soundly refuted now)

* Irreducible complexity of the eye (not only refuted but demonstrated to have occurred dozens of different ways)

* abiogenesis of pyrimidine ribonucleotide claimed to be impossible (refuted "Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions"; Nature 459, 239-242 (14 May 2009))

* abiogenesis of ribose claimed to be impossible (refuted "Selective derivatization and sequestration of ribose from a prebiotic mix"; Greg Springsteen and, Gerald F. Joyce; Journal of the American Chemical Society 2004 126 (31), 9578-9583)

But theories about abiogenesis are a completely different question.

#2 Evolutionary theory itself is a fairly simple set of ideas:

A) Organisms change subtly from generation to generation, this natural variation is very easy to observe (e.g., in the HUGE variety of breeds of dogs human have created)
B) Only those organisms which are able to survive and reproduce will have their traits passed on to the next generation (in Darwins time genetics was not yet understood, and RNA and DNA provide the explanatory power of How this process works -- this was a HUGE confirmation of the theory). This is often called Natural Selection (and often misrepresented as Survival of the Fittest, although more correctly it is survival of those organisms which are adapted to their environment). If you have a mutation that makes it nearly impossible for you to breath and you die that mutation is much less likely to survive in the population, whereas the more rare (but frequent enough) mutations that confer some survivability to an organism tend to spread through the population.
C) Over extremely large timescales those smaller changes would add up not only to completely different species but all the variety of life we see today

There are specific scientific claims associated with those ideas but that's the nutshell version.

One of the major, modern lines of confirming evidence to (C) is the observed mutation rate of DNA compared against the level of 'drift' observed in different species which also aligns very well with the fossil record.

ALL of the different types of DNA mutations required to explain the varities of DNA we observe today are pretty well understood.

The Major things that can happen to DNA is:

a) a whole gene can get duplicated, this leaves either the copy or the original functional why the other one might begin to mutate in other ways
b) base substitution -- can subtle change a single amino acid which can subtly or profoundly change the action of the gene
c) base insertion/deletion in a gene -- this COMPLETELY changes the protein generated by that gene substantially (from the point of insertion on). Initially this gene/protein may be non-functional (but subject to later mutations)
d) chromosome's can split into two, or two can join into one (for a PERFECT example of this Humans have 23 pairs of chromosomes while chimpanzees have 24 but they align fairly well: http://www.gate.net/~rwms/hum_ape_chrom.html)


And finally, one very common confusion on understanding evolution is what does a "New" species mate with, it would be the only one right? But that's not at all how things work, remember *each* step is (usually) fairly small, it's only after a lot of steps over a long time and usually with two populations getting isolated from each other that we would (generally) expect to see a new species emerge.

Just look at the human population. There are couples who are both healthy but CANNOT conceive a child with each other -- but with a sperm donor the woman can conceive -- sometimes the reasons for this are that they are simply not compatible at the DNA level. If you isolated populations of those two people for 100,000 years those two populations would probably be completely unable to interbreed. So it's really more of a subtle difference at first. It is NOT like a dog has a cat for a baby. If such a thing happened it would disprove evolutionary theory. Nor did humans evolve FROM chimps, but we DID have a common ancestor a LONG time ago.

I hope these thoughts assist you in your goal. Don't take my word for ANY OF IT. Look it up! I could be wrong on some points! (sorry for any typos/errors but this was just off the top of my head + a few internet searches -- google is your friend).

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Permalink Reply by Loop Johnny on November 21, 2010 at 9:09am

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