TalkOrigins.org and other Sources

I am posting a few links for a friend. They might also interest my other readers.

The first links to the online version of an article originally printed in the journal Natural History, issue 111(3) pages 73-80, in April 2002. It discusses Intelligent Design and covers topics such as irreducible complexity, specified complexity, and the proposed difficulty of natural selection to produce new features and new species. The articles is republished on the web by actionbioscience.org.

http://www.actionbioscience.org/evolution/nhmag.html

The next link leads to the Talk Origins Archive, a newsgroup archive of articles that deal with the creation/evolution debate and other related themes. The tone the authors take, I have found, is non-antagonistic toward religion itself, only toward those who attack the sound concepts of biology and other sciences. I would say most if not all of the authors allow for or subscribe to a belief in Deity themselves. The articles tend not to be quite as well polished as textbook standard, but the info is well researched and very reliable. The website contains review articles and to my knowledge does not allow original research.

Before I give the link, I will warn that the reader will see the word creationist used often. Understand that this label refers to a group of religious persons that believe in a very strict and literal interpretation of the biblical book of Genesis and that wholly reject the concept of biological evolution and much of the geological and astronomical sciences. The word creationist here does not refer to just anyone who believes the universe was created by Deity.

Here is the home page:

http://www.talkorigins.org/

I recommend the FAQs page to help orient the reader:

http://www.talkorigins.org/origins/faqs-qa.html

Here I quote one of the questions with its answer from this page. "Q: Don't you have to be an atheist to accept evolution? A: No. Many people of Christian and other faiths accept evolution as the scientific explanation for biodiversity."

The introduction to evolutionary biology will help the reader build a basis for understanding and discussing the topic.

http://www.talkorigins.org/faqs/faq-intro-to-biology.html

Check out the five major misconceptions about evolution:

http://www.talkorigins.org/faqs/faq-misconceptions.html#observe

I found the following article interesting. It gathers instances of observed speciation and explains why lists like this one are uncommon. Section 3.0 is especially helpful.

http://www.talkorigins.org/faqs/faq-speciation.html

Lastly, after logos is satisfied, make sure ethos gets its fill by checking out the awards page:

http://www.talkorigins.org/faqs/awards/

The last link I will post sends us to a famous article written in the 1970's by Theodosius Dobzhansky, a christian and biologist who died in 1975. The article is titled, "Nothing in biology makes sense except in the light of evolution." Dobzhansky's logic is sound and despite the passage of more than thirty-five years it remains most relevant and accurate today. The article is reproduced by PBS.

http://www.pbs.org/wgbh/evolution/library/10/2/text_pop/l_102_01.html

Scroll to the bottom of the page for the reference of the original publication.

I hope my readers enjoy these sources and will appreciate the importance of becoming acquainted with them.

Artificial Life

Craig Venter is the guy that headed the Human Genome Project. Since the completion of that project he has been working on creating artificial genomes and life. Check out the news article and the journal article:

http://www.reuters.com/article/idUSTRE64P6OZ20100526

http://www.sciencemag.org/cgi/rapidpdf/science.1190719v1.pdf

Watch this video, it is very helpful:

http://www.guardian.co.uk/science/2010/may/20/craig-venter-synthetic-life-form

This accomplishment repressents an important part of theoretical biology made reality. The possible utility of this technology in the future are nearly endless.

Homo neanderthalensis: the Genome has Arrived

(Photograph used with permission by the copyright holder under GFDL.)

Four years ago I heard that a group of anthropologists had started on a project to sequence the Neanderthal genome. I was amazed. Many had their doubts and the researchers faced immense obstacles. Two years into the project, it had lost momentum and I accepted that the dream had failed.

Today I picked up this article from the journal Science: http://www.eva.mpg.de/neandertal/press/presskit-neandertal/pdf/Science_Green.pdf

More to come later. I needed to publish this immediately. Expect the world to change.

Later:

You may wonder why this is significant. Neanderthals and humans overlapped geographically and chronologically. They are our closest relatives in the fossil record and had similar lifestyles. However, humans were able to surpass Neanderthals in many aspects. Eventually, Neanderthals disappeared and only we remained. We do not completely understand what gave us the advantage over our non-human relatives, but studying the genome of this extinct species promises great insight into why.

Lets look at the article together.

The journal Science is unique in that it publishes studies from all disciplines of science and includes only those studies most important to the entire scientific community and also to the general public. The articles in this journal maintain high standards while modifying the standard format slightly to make the material accessible to non-specialist readers. The study by Green et al. that we will discuss mixes methods with discussion and conclusions instead of giving all of the methods in one sterile block, making it easier to follow.

We will start on page 715. The authors identify differences in protein structure that make humans different from Neanderthals. The first gene discussed, SPAG17, plays a role in  the flagellum of sperm, indicating that Homo sapiens sperm swim differently than that of H. neanderthalensis. Differences in PCD16 show that H. sapiens' wound healing process may differ from H. neanderthalensis. TTF1 is interesting because it helps regulate transcription of genes, meaning that it affects the way that all proteins are constructed from our DNA. This one gene has the potential to affect all other protein coding genes across the entire genome. Changes in RPTN indicate a difference in the epidermis, sweat glands, hair roots, and taste buds.

Also of note is TRPM1 that has lost functionality in some humans but is functional in Neanderthals. This gene codes for, in short, skin pigmentation.
The authors then focus on regions (called HARs) identified as being stable throughout the history of other vertebrates but that underwent many changes in H. sapiens. These areas should give clues about what makes us physiologically different from other animals, including H. neanderthalensis. Forty-five of these HARs were identified as being different in humans from the Neanderthal sequences. Not much is known about these regions, so the authors were unable to comment on them; however, they show great potential for further insights.

We skip to page 717. The authors investigate 20 regions in the human genome that have experienced heavy selective pressures relative to Neanderthals. The first five do not contain protein-coding genes and may be regulatory or structural in function. (Ask me about gene regulation and DNA structure and packaging if you are interested.) The most heavily selected on the remaining 15 regions contains the gene THADA, which has been associated with type II diabetes. This shows that human metabolism likely differs from Neanderthals. Other genes in these selected regions have been associated with diseases like Down syndrome, schizophrenia, and autism. Changes in these genes and regions would have created cognitive differences between the two species. The last gene discussed that has undergone heavy selection is RUNX2, which is responsible for the disease cleidocranial dysplasia. In short, this disease causes abnormal skeletal formations including an enlarged, protruding frontal bone (forehead or brow); heavy clavicles resulting in a change in the shoulder joint; and a bell-shaped rib cage. This one gene shows how some major skeletal features changed in humans.

The last half of the paper deals with multiple methods used to demonstrate the same results. The authors say it best:

"We find that the Neandertals are equally close to Europeans and East Asians.... However, the Neandertals are significantly closer to non-Africans than to Africans."

Multiple hypotheses can account for this, but the most likely scenario says that H. neanderthalensis interbred with H. sapiens some time during their overlapping histories but posterior to speciation. Because of this, a small percentage of Neanderthal DNA is present in the human population today.

The Neanderthal genome has initially created many more unanswered questions than those it has helped answer. The next few years (or couple of decades) will tell us much more of who Neanderthals were and what made the difference between our survival and their demise.

Supergame XXXIX

Here is some footage from the game we went to earlier this month:

Indie Short Films

The National Film Board of Canada is holding a short film competition. Here I post my two favorites. Jenny said she didn't understand them and Jeff got scared and ran away. With whom am I to discuss art?

My Favorite News Casters

If you don't know what Onion News Network is, you need to look up some of their videos. Here are some samples:








Warning: Don't watch this one unless you are feeling unusually intrepid-->

Battle of the Black Sea

This excerpt is from the epilogue of Mark Bowden's book Black Hawk Down:

Aidid died in 1996 without uniting Somalia under his rule, a victim of the factional fighting the UN had tried to resolve. His clan still struggles with rivals in Mogadishu, trapped in the same bloody, anarchic standoff. Clan leaders I spoke with in that destroyed city in the summer of 1997 seemed to think that the world was still watching their progress anxiously. Photographer Peter Tobia and I were the only guests at the Hotel Sahafi during most of our stay there. We were the first and only Americans who have returned to Mogadishu trying to piece together exactly what happened. I told the Habr Gidr leaders who were hostile to our project that this would likely be their only chance to tell their side of the story, because there weren't journalists and scholars lined up at the border. The larger world has forgotten Somalia. The great ship of international goodwill has sailed. The bloody twists and turns of Somali clan politics no longer concern us. Without natural resources, strategic advantage or even potentially lucrative markets for world goods, Somalia is unlikely soon to recapture the opportunity for peace and rebuilding afforded by UNOSOM. Rightly or wrongly, they stand as an enduring symbol of Third World ingratitude and intractability, of the futility of trying to resolve local animosity with international muscle. They've effectively written themselves off the map.

Mark deserves much praise for his pain and efforts to maintain objectivity and fidelity in his retelling of the Battle of the Black Sea. I often admire the level of professionalism demonstrated in the writings of journalists, but Mark's work on this project stands above all others I have read.

"Whoever does not have the stomach for this fight, let him depart. Give him money to speed his departure since we wish not to die in that man's company. Whoever lives past today and comes home safely will rouse himself every year on this day, show his neighbor his scars, and tell embellished stories of all their great feats of battle. These stories he will teach his son and from this day until the end of the world we shall be remembered. We few, we happy few, we band of brothers; for whoever has shed his blood with me shall be my brother. And those men afraid to go will think themselves lesser men as they hear of how we fought and died together." From Henry V, by William Shakespeare.