Misanthropy

I did not write this article. It was written by beskeptical on the Bad Astronomy Forums. It is an excellent read if you still have doubts about evolution. Creationism is a joke. God did not create the world in 6 days, nor is the planet 4000 years old. This is a fantasy story that should be kept in the books, unfortunatley schools are teaching creationism in place of or in addition to evolution. They also declare that evolution is not fact, cannot be proven and should not be considered heavily. When making claims that go against the mainstream the burden of proof always falls to the person making the claim. A good reason for that is most non-mainstream claims are outlandish. Oddly enough, whenever debating with Creationists and god believers they demand that aethists and evolution believers to provide the proof. The outlandish claim here is not by scientist who believe evolution. The outlandish claim is that there is an all powerful being hiding from —- This is best saved for another article.

Read on.

Why Evolution is no longer in question.

In the last decade, genetic research has advanced at an accelerating pace. In the information age we live in, tremendous scientific breakthroughs are occurring but there is often a delay before the results are widely known. This is the case with genetic research that has revealed the mechanisms for evolution and thereby confirmed the theory beyond reasonable doubt.

The theory of evolution emerged 100+ years ago. At the time, it was not completely understood, nor was it accepted as a certainty as the evidence was only beginning to be discovered. But evidence has since accumulated. Genetic research has unlocked the digital code that life uses to start, grow, function, and reproduce. Changes in that digital code result in evolution of life.

Yet people still believe, and, are still teaching children that evolution is only one of many hypotheses explaining life. In addition, arguments against evolution are still put forth that are no longer valid. It is time to explain a few things about how solving the code of DNA has explained the mechanisms of evolution and made the theory no longer in question.

A brief history

‘The fittest survive’ was the first explanation Darwin concluded from his observations. Less well known was Mendel, who in 1866, theorized the principles of heredity. Biological traits were inherited through factors (now called “genes”). His research with plants showed traits were inherited, one from each parent, which did not mix nor blend but remained segregated. In the Netherlands, Hugo de Vries proposed a new theory of evolution known as mutationism.

As these theories emerged, evolution was thought of as an oversimplified process. An analogy can be made to thinking electrons ‘orbit’ the nucleus when in reality, the process isn’t that simple. Simplified versions leave lots of questions how the process works.

Then a very big breakthrough came when technology was developed that could easily isolate and manipulate tiny fragments of DNA. Shortly thereafter, rapid advances were made and the genetic code was literally broken. Translating the code has now begun. Many advances have been made in translation which will not be discussed here.

You can think of DNA code in the same way as you think of computer code. If you found a computer in a cave and didn’t have any experience with computers, you might do lots of experiments and after a period of time figure out lots of functions. But one day you figure out the digital code that each program uses. Now you are on a whole different level of understanding about computers. With DNA code deciphered, we are on a whole different level of understanding evolution.

How genes work

All living organisms have a DNA or RNA map that contains all the instructions for building that organism.There are billions of lines of digital code in DNA. There are 4 amino acids in various combinations which make up the code. Humans have about 3 billion base pairs of the 4 amino acids in their DNA map. When the DNA code changes occur, detrimental changes die out, neutral and successful ones go on reproducing. Changes accumulate over time. That is the simple version.

But what additional information is now known about the process?

Segregated function

One question the theory of evolution must answer is how do changes accumulate and still function? How do single mutations change fins to limbs to wings?

The answer is in how genes are structured. Genes are divided up. Where a scale goes (covering), how it forms (embryo), what it does (protects the inside), what structures are within (like oil glands), and what it looks like (camouflage or attract a mate or both) are just a few examples of things that are controlled by separate genes.

If you make a very small change, you can get a very big functional result. Take the mutation that causes a person to have 6 fingers or toes. The only change that has to occur is in the number of digits. All the rest of the structure of a finger is encoded in separate genes.

Separate genes have been found to work in more than one species. You can put a rabbit embryo gene that directs the growth of the eye into a fruit fly embryo which has had the equivilent gene removed. You get a normal compound fruit fly eye in the right place.

The same genes continue to function and remain the same even as the organism evolves into another species. We are using the yeast genome to find human genes. The yeast is a much simpler organism yet many of our genes are the same!

Fruit fly genes can be manipulated to get antenna where legs belong or legs where antenna belong. The gene that initiates a leg or an antenna is separate from the gene that determines what an antenna or leg are. As little as one change in one amino acid on any DNA strand can impact a change in the organism.

What it boils down to is as the gene code is deciphered, the mechanisms to get limbs, whether wings or arms, is essentially the same from organism to organism. The basic structure is then modified by the specific additional genes. It’s sort of like the underlying structure of a wall with different wallpaper.

Single mutation, huge impact, small impact or no impact

Another stumbling block in understanding evolution is understanding what single amino acid changes in the code can do. The change may do nothing since there is a lot of redundancy built in to the code. The change may have a small, moderate, or large impact if it changes the code in a critical place. And, a change may have a large impact by turning a gene on or off completely.

Mutations are not always single amino acid exchanges. Sometimes the gene may lose or gain a whole strand of DNA.

How mutations occur

There are several ways new information is created when DNA replicates.

1) steady rate of errors in copying:

Every time a cell divides an error can occur. In a developing fetus, a complete change can result. In a grown organism, you can get things like cancer developing.

2) recombining DNA during sexual reproduction:

Different combinations of DNA, even if no new material were to result, spread genetic changes into larger populations. In reality, genes from the mother and father are not always either or. Sometimes the combination differs from the two original genes because of interaction with eachother. Brown eyes plus blue eyes might result in hazel.

3) acquiring new DNA:

This occurs in other ways besides sexual reproduction. A virus is made of either DNA or RNA. When a cell is infected the DNA or RNA can become part of the infected cell’s DNA or lead to the creation of new DNA in the infected cell. When you have a cold sore that recurs, you are not getting a new infection, the virus has moved into your cells permanently, and is now part of that cell’s genetic code.

4) losing DNA:

Whole pieces of DNA might become inactive due to a simple amino acid copy error. Whole pieces might break off.

5) bacteria and viruses have special mechanisms:

Bacteria exchange genetic material with unrelated species via ‘plasmids’, (little packets of genetic material). Some single celled organisms exchange genetic material as offspring are produced. Some organisms fuse their genetic material and some viruses exchange whole genes when 2 strains infect the same host. It amounts to gene shuffling.

Selection processes

Selection forces or pressures determine the path evolution takes. Mutations occur like clockwork. Some genetic molecules are more stable and some mutate more readily. The environment, diseases, mates preferences, and purely random occurances are the main selection processes which determine which genetic changes will proliferate.

Successful traits are not necessarily single function traits. Sometimes a beneficial trait will have a detrimental trait combined with it. The overall process should be viewed with the complexity it contains.

The more mutations, and, the more frequent & number of offspring, the more successful the organism is in adapting to changes in the organisms’ biosphere. Variability has been shown to be more successful than too much specialization since a varied population is more likely to have survivor traits should the species be threatened.

Life evolves at different speeds. Major extinctions narrow the genetic line which starts again with a smaller number of individuals. Animals migrate and become isolated from other groups. Food sources come and go leading to lots of variation. During human evolution, genetic evidence shows the human population was once large but was reduced to as few as a thousand members then repopulated the planet.

Irreducible complexity argument

How can random genetic changes go from a scale to a feather if there is no function of the inbetween structure?

Irreducible complexity is not supported by the evidence. The eye doesn’t seem to be irreducible, but when you look at examples in nature, it turns out the evolution of the eye really can be traced back to its very beginnings as a mere light sensitive cell. The problem here is conceptualizing the transitions, it isn’t that the transitions do not exist.

Transitional traits are all around. All forms of circulatory systems exist today. Animals that live in and out of the water, in salt water and in fresh water, colonies of cells that act as an organism, colonies of cells that have symbiotic relationships with other species and act as a connected organism are some examples.

1st molecules to whole organisms

After the last big blast of asteroids that resurfaced the Earth, (~3.9 billion years ago), fossil evidence shows that life was well established only 50 million years later. After another 350 million years sophisticated microbes were alive. “Molecular fossils from Greenland tell us that some kind of life was on Earth … by 3.85 billion years ago. Scientists can’t say exactly what sort of life was leaving its mark in Greenland, but it was already altering the chemistry of the oceans and the atmosphere on a global scale” (Zimmer, see references below)

The fossil and geologic evidence supports a beginning soup of amino acids turning into a soup of RNA strands turning into a soup of loose gene like structures turning into a soup of redundant and ever mixing genes until whole organisms appeared. The evidence supports RNA as the first organic structure from which DNA and later complete organisms evolved.

Gerald Joyce at the Scripps Research Institute, along with other scientists, started with RNA molecules in the late 80s and replicated it into 10 trillion variations. He mixed those with DNA molecules. He took the few RNA molecules that interacted with the DNA and made 10 trillion more variations. After 2 years he had close to the same RNA-DNA interactions that occur in cells today.

The family bush

The original thoughts on how evolution progressed were made by biologists. The addition of genetic science has expanded the original hypotheses of single branches from the beginning to single branches after a tangled root system. The three main branches of the bush that emerged are Bacteria, Archaea, and Eukaryotes.

Only one of the branches grew into multicelled organisms which includes humans. We can map the DNA and see the relationships of all organisms. Plants, it turns out are close relatives of animals and are from the same branch, Eukaryotes.

Some genes have been conservered from the earliest organisms to present day organisms. What that means is when those genes mutate, the result is unlikely to be viable. What it also means is many of our genes are the same in diverse organisms like fruitflies and yeast cells.

Humans’ genome mapping shows how we are related to plants and animals, where our ancestors migrated from, where back in evolution humans and fruit flies are descended from the same ancestor, and any other question you want to answer about our family bush.

One of my favorite all time discoveries, is that genetic research has shown humans to be all one race. The amount of genetic difference it takes to have the appearance of separate races as most people have come to believe is too small to actually be considered relevant.

Humans have about 3 billion base pairs of amino acids in their DNA. The number of those base pairs differ by about .01% between any two humans, whether they are black and white or black and black; whether they come from the same village or from different continents.

Skin color and facial features don’t indicate different human races any more than blood types do.

Examples and references

I suggest “evolution, The Triumph of an Idea”, by Carl Zimmer, 2001. It has a very good detailed description of the process of evolution and the state of the science of evolution today. And it isn’t too technical.

Since I couldn’t find many references that were written for the majority, here are some technical but enlightening examples. There are thousands more. Just ask google for genome or genetic research.

http://zygote.swarthmore.edu/droso4.html

SPECIFICATION OF ORGAN FATE IN DROSOPHILA: HOW ANTENNAPEDIA DISTINGUISHES BETWEEN ANTENNAL AND LEG FATES

References from the above linked article:

Casares, F. and Mann, R. S. 1998. Control of antennal versus leg development in Drosophila. Nature 392: 723 - 726.

Morata, G. and S?nchez-Herrero, E. 1998. Pulling a fly’s leg. Nature 392: 657 - 658.

Schneuwly, S. Kuroiwa, A., and Gehring, W. J. 1987. Molecular analysis of the dominant homeotic Antennapedia phenotype.EMBO J. 6: 201 - 206.

Struhl, G. 1981. A homeotic mutation transforming a leg into an antenna in Drosophila. Nature 292: 635 - 638.

http://zygote.swarthmore.edu/limb2.html

FGF-10 AND THE INITIATION OF THE VERTEBRATE LIMB

Reference:

Ohuchi, H. and eleven others. The mesenchymal factor, FGF10, initiates and maintains the outgrowth of the chick limb bud through interaction with FGF8, and apical ectodermal factor. Development 124: 2235 - 2244.

http://zygote.swarthmore.edu/limb1.html

RECRUITING MUSCLE CELLS FOR THE LIMBS

References:

Bladt, F., Riethmacher, D., Isenmann, S., Aguzzi, A., and Birchmeier, C. 1995. Essential role for the c-met receptor in the migration of myogenic precursor cells into the limb bud. Nature 376: 768 - 771.

Chevallier, A., Kieny, M., Mauger, M. and Sengel, P. 1977. Limb somite relationships: Origin of limb musculature. J. Embryol. Exp. Morphol. 41: 245 258.

Christ, B., Jacob, H. J. and Jacob, M. 1977. Experimental analysis of the origin of wing musculature in avian embryos. Anat. Embryol. 150: 171 186.

Daston, G., Lamar, E., Olivier, M., and Goulding, M. 1996. Pax-3 is necessary for migration but not differentiation of limb muscle precursors in the mouse. Development 122: 1017 - 1027.

Geduspan, J. S. and Solursh, M. 1992b. Cellular contribution of the different regions of the somatopleure to the developing limb. Dev. Dynam. 195: 177 187.

George Weinstein, M., Decker, C. and Horwitz, A. 1988. Combinations of monoclonal antibodies distinguish mesenchyme, myogenic, and chondrogenic precursors of the developing chick embryo. Dev. Biol. 125: 34 50.

Hayashi, K. and Ozawa, E. 1995. Myogenic cell migration from somites is induced by tissue contact with medial region of the presumptive limb mesoderm in chick embryos. Development 121: 661 - 669.

Itoh, N., Mima, T., and Mikawa, T. 1996. Loss of fibroblast growth factor receptors is necessary for terminal differentiation of embryonic limb muscle. Development 122: 291 - 300.

http://www.jgi.doe.gov/News/news_12_12_02.html

Sea Squirt DNA Sheds Light on Vertebrate evolution

Genome of Ciona intestinalis Yields New Insights Into the Origins Of Complex Biological Systems

Press Release: December 12, 2002

For More Information Contact:

Charles Osolin (925) 296-5643

osolin1@llnl.gov

Photos Available at: http://www.jgi.doe.gov/xpress/ciona_pics/

“In an article for the December 13, 2002 issue of the journal Science, an international consortium of researchers reports on the draft sequencing, assembly, and analysis of the genome of C. intestinalis. The consortium is led by the U.S. Department of Energy’s Joint Genome Institute (JGI); the Department of Molecular and Cellular Biology and Center for Integrative Genomics at the University of California, Berkeley; the Department of Zoology at Kyoto University, Japan; and Japan’s National Institute of Genetics in Mishima. It includes nearly two dozen other research institutions.

By comparing Ciona’s genome with those of the human and other animals, the researchers were able to glean new insights into the evolutionary origins of the human brain, spine, heart, eye, thyroid gland, and nervous and immune systems, as well as a better understanding of chordate and vertebrate development in general.”

**

Media contact:

Charles Osolin, JGI, 925-296-5643, osolin1@llnl.gov

Scientific contacts:

Dr. Eddy Rubin, JGI, 925-296-5650, emrubin@lbl.gov

Dr. Dan Rokhsar, JGI, 925-296-5797, dsrokhsar@lbl.gov

Dr. Paul Richardson, JGI, 925-296-5851, pmrichardson@lbl.gov

Dr. Jeffrey Boore, JGI, 925-296-5691, jlboore@lbl.gov

Dr. Michael Levine, University of California at Berkeley, 510-642-5014, mlevine@uclink4.berkeley.edu

Dr. Nori Satoh, Kyoto University, +81-75-753-4081, satoh@ascidian.zool.kyoto-u.ac.jp

Dr. Yuji Kohara, National Institute of Genetics, +81-559-81-6854, ykohara@lab.nig.ac.jp