DNA 101: Deciphering Biological Information

I just finished reading Chapter 9: Evidence of Biological Information for this Sunday. You should all be happy to know that it is relatively short! When you are reading through this week’s material, I suggest that you read it once maybe straight through trying to get the general gist of what is being said. Strobel tries to emphasize the point that the molecule holding our genetic information, DNA, is extremely complex and would require an intelligent source to create diversity  for the molecules that make up our cells. He examines the way a molecule might be developed gradually, such as self-organization. However, go back and do some research because I believe it is important that you understand how DNA functions, at least to a basic degree, so that you can be amazed at its complexity! On Sunday I will be prefacing our conversation with a DNA 101 session. I want to throw out there that genetics is a quickly growing topic. Our knowledge base has exploded since the discovery of the structure of DNA in 1953 and more recently grown with the completion of the Human Genome Project in 2003. So if you feel like this is foreign and new to you, it’s ok! It’s kind of new to everyone!

                 

Here are some resources to help as you read.

> http://www.nature.com/scitable/topicpage/dna-is-a-structure-that-encodes-biological-6493050

    Broad overview of DNA components and structure

> http://www.ornl.gov/sci/techresources/Human_Genome/project/info.shtml (down to the horizontal line only)

> http://ghr.nlm.nih.gov/handbook

   Feel free to look at everything, but specifically:

   -Cells and DNA; ii. What is DNA?; iv. What is a gene?; What is a chromosome?

   -How Genes Work: i What are proteins and what do they do?; ii. How do genes direct the production of proteins?; iii. Can genes be turned on and off in the cells?

> http://www.brooklyn.cuny.edu/bc/ahp/BioInfo/SD.Geno.HP.html

   See “Flow of Information” and “Genetic Code”

> OR A VIDEO--http://www.youtube.com/watch?v=-ygpqVr7_xs (The Central Dogma)

   http://www.youtube.com/watch?v=D3fOXt4MrOM&NR=1&feature=endscreen (DNA to proteins)

And for some laughs……http://www.youtube.com/watch?v=_Q2Ba2cFAew (Central Dogma Song)

When we talk about DNA, we are talking about a double helical structure which is similar to a ladder twisted to resemble a spiral staircase.

http://www.mhhe.com/biosci/esp/2001_gbio/folder_structure/ge/m4/s1/assets/images/gem4s1_1.jpg (DNA structure)

http://www.sciohio.org/Image84.jpg (twisted ladder)

The sides of this ladder are made up of two components, a sugar and a phosphate, that alternate to make a sturdy backbone. The rungs of this ladder are formed by specialized pieces known as nitrogenous bases. There are four nitrogenous bases: A, C, T, and G also known as adenine, cytosine, thymine, and guanine, respectively. These four letters function to as the information source for the proteins necessary to the cell. These letters are independently arranged along the length of the sugar-phosphate side rails. However, in pairing up to form a complete rung, only specific interactions may take place. (A goes with T; C goes with G). The interaction between the bases (hydrogen bonds) knits together the two strands of DNA to form the double helix.

 So DNA acts as the holder of all our genetic information and resides in the nucleus of the cell. But how is this information extracted so that it can be put to use?

http://www.bio.miami.edu/~cmallery/150/gene/central.dogma2.jpg

http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/images/central_dogma.gif

This takes us to a little thing known as the Central Dogma. The Central Dogma describes the process of moving from DNA to proteins.

Our journey starts with the need for a particular protein. When this happens, a complex of proteins assembles on the stretch of DNA that corresponds to the protein in need. The DNA is unzipped so that a single strand (a backbone with attached bases) can act as a template for creating a new strand, known as messenger RNA, or simply mRNA. Messenger RNA closely resembles DNA. It has a sugar phosphate backbone with attached nitrogenous bases. The most notable difference is a substitution of U (uracil) for T (thymine). Then, units known as nucleotides (which consist of a sugar+phophate+nitrogenous base) are fit like puzzle pieces to the matching template on DNA. Once the stretch of DNA is paired in a complementary fashion , the mRNA is released. This mRNA will be processed and then leaves the nucleus so that it may proceed to the factory-like unit known as the ribosome.

http://www.phschool.com/science/biology_place/biocoach/images/transcription/startrans.gif

The ribosome is the site of protein synthesis. The process of creating mRNA is known as transcription. The next phase where mRNA is used to manufacture proteins is known as translation.

Back to the story…mRNA moves out of the nucleus and travels through the interior of the cell until it encounters the ribosome. As the ribosome pulls the mRNA through its subunits, proteins are made in an intricate process involving a three-letter code. These three letter codes, known as codons, correspond to one of twenty amino acids. There are 64 codons that are used in building proteins. How is this done, you ask?

http://hyperphysics.phy-astr.gsu.edu/hbase/organic/imgorg/translation2.gif

There are special players known as transfer RNA, or tRNA. Transfer RNA is responsible for matching the right amino acid to each codon. They do this through a structure known as the anticodon. Each tRNA has a three letter anticodon that can be matched (again, kind of like a puzzle piece) to its complementary codon. So in the depths of the ribosome, tRNAs are matching up and moving out, leaving behind their amino acids on a growing peptide chain. Once all the amino acids are assembled, a protein is released.

                  Viola! Through the complexity of DNA we have arrived at a protein.

Hello everyone! I hope your week is going well and you are having multiple opportunities to talk to others about the subjects we have been discussing ( :] please post in Reflect Here --------------->). This Sunday we will be moving through chapters 7 and 8 of Case for a Creator. We will be focusing on the fine-tuning of the Universe and evidence of design in nature.

These might be some helpful terms to research before then:
-anthropic principle
-argument from design
-arguments on poor design/dysteleology (retina, panda's thumb, etc.)
-Copernican Principle
-Habitable Zones
-black box
-irreducible complexity
-self organization

I also posted a youtube link in the Weekly Materials section (--------------->). Several of you asked about the videos we watch in class. These are simply excerpts from a larger series by Lee Strobel entitled "The Case for a Creator: A Six-Session Investigation of the Scientific Evidence That Points toward God". This series along with a participant's guide can be purchased through Zondervan if you are interested in having a copy yourself. The link I posted is an older version of this series. Due to copyright laws, we cannot post videos from the DVD provided with the curriculum. As always, I look forward to meeting and discussing on Sunday at 10:55! If you have any questions feel free to email us or comment on the blog.

Nicole

Icons

Today we talked about Case for a Creator Chapters 2 and 3 dealing with the iconic images of evolution. He spends quite a bit of paper explaining to the readers what these images themselves are, but ultimately his message seems to be one that urges Christians and scientists alike to just talk about them.  As he progresses, Strobel weaves a story that is familiar for many lost souls. As a child he is particularly influenced by the Stanley Miller experiment which acted as a foundation for other images to accumulate and make it possible for him at a young age to discount the existence of a creator.

Unfortunately, this is happening in classrooms every day. Even though some of these examples have been discredited or sufficiently doubted, they are still being presented in a way that can be perceived as very factual to those that are searching for answers, especially if they are looking for a way around answering to God. I think we all need to develop a sense of personal responsibility and teach our children (or in my case, somebody else’s children lol) and engage them in conversation about what they are learning in the classroom and from their friends.

While there are many more of these icons out there for discussion, Lee Strobel focused on the following images. I include the page numbers for a ‘full-size’ copy of the book. However, I realize that many of you may have received a smaller version when signing up for the class so I will try to snag a copy and include those as well later on!

                  1) Stanley Miller Experiment (p. 19, 37-41)

                  2) Darwin’s Tree of Life (p. 19-20, 42-47)

                  3) Haeckel’s Embryos (p. 20, 47-52)

                  4) Archaeopteryx (p. 21, 55-60)

                  5) Homology in Vertebrate Limbs (p. 35, 52-54)

                  6) Kettlewell’s Peppered Moths (p. 35)

                  7) Darwin’s Finches (p. 35)

                  8) Java Man/Hominid Fossils (p. 54-55, 61-64)

                  How many of these icons have you been exposed to? One? Two? Or in my case, all of them? (Feel free to assume as a literal or rhetoric question...there is always that comment section or the Reflect Here page for thoughts such as these!)

When reading or re-reading these chapters, or even in conversations about the individual images, I encourage you to embrace the controversy associated with each. Most of these have limited evidence and require some faith in conclusion making. To some pre-Christians these images are what they have solely based their conclusions about evolution on and it might be beneficial to ask them to examine them more closely. If the hinge-pin of a belief starts to decay or is removed completely, what a better time to bring someone to the conclusion of a creator and help them know our God and Maker of the Universe! Praise God for inventing Google so that we literally have a constant stream of information at our fingertips for our perusal and use in witnessing to the scientific community! I personally like to read both sides of the story; that is, I like to see where an evolutionist and non-believer would have developed their understanding so I can better approach and meet them with alternative interpretations. It can become a little daunting and perhaps even disheartening if you stumble upon someone with a very anti-Christian stance in the literature, but God is always there to strengthen my resolve in prayer.

I’m going to back up a bit and just sort of proceed through the chapters so I can hit a few points in the reading that may have not been addressed in our discussion this morning.  In chapter 2, Strobel really just states that it was his interest in science that led him to be receptive to the concept of macroevolution and then to jump to atheistic claims. As he is describing four of the icons, Strobel writes, “The moment I first learned of Miller’s success, my mind flashed to the logical implication: if the origin of life can be explained solely through natural processes, then God was out of a job!” (p. 19). This is not to say that a belief in the Theory of Evolution always goes hand in hand with the belief of atheism, but it can act as an easy avenue for someone searching to maintain control and avoid answering to a higher power if they are presented with an opportunity to remove God from the equation. In fact, Strobel quotes philosopher Daniel Dennett claiming that “Darwinism is a ‘universal acid’ that ‘eats through just about every traditional concept and leaves in its wake a revolutionized worldview’” (p. 24).

Chapter 3 is pretty much all about addressing the icons in some detail. Strobel frequently references Icons of Evolution by Johnathan Wells published in 2000. In tackling these icons and presenting a case against evolution, Wells has experienced much criticism from the scientific community (see “Critics Rave Over Icons of Evolution” http://www.discovery.org/a/1180 Spoiler: it's not a good kind of raving). Many people have attempted to dissect these icons and whether or not these examples should be included in textbooks because of the false conclusions it can lead students to form. While I agree that learning often requires us to learn simplified and often incomplete or incorrect models to facilitate our comprehension of a more abstract concept, this sort of misrepresentation causes the young Lee Strobel’s of the world to glean false evidence for evolution.

I’m going to try and briefly address each of the icons in this post. I have included resources on the handout for this week which can be found under the Weekly Materials page on the right hand side of the blog page. If you find an image that is particularly poignant or has frequently been presented in conversations with friends and family, definitely do some research so you can feel more comfortable on the next go around. One more thing learned is another tool to use in the future.

Stan Miller: We don’t know what the atmosphere was for originating amino acids. It’s not necessarily the one simulated by Miller, but not necessarily contrary. There has recently been renewed interest in the experiment by Bada and Lazcano in the 2000s supporting the original setup. But guess what? Man has limited understanding and we may never know the prebiotic atmosphere of the Earth. Regardless, a mechanism of how amino acids would develop into the first cell is still very inconclusive.

Darwin’s Tree of Life: When Googling images, I was struck by just how many people had Darwin’s original tree of life tattooed on their bodies…One of the biggest challenges to the tree of life is the Cambrian explosion and other inconsistencies in the fossil record. There is always debate over the presence of transitional forms, or missing links, such as Archaeopteryx. We see an emergence of the major phyla in the Cambrian period and there is relatively little diversity in strata prior to this. Some people refer to this as a lawn arrangement rather than the branching tree that Darwin proposed. “A key aspect of his theory was that natural selection would act, in his own words, ‘slowly by accumulating slight, successive, favorable variations’ and that ‘no great or sudden modifications’ were possible” (p. 43). You might want to also dig into the concept of punctuated equilibrium as this has been cited as an explanation for the Cambrian explosion recently.

Haeckel’s Embryos: Basically, Strobel says there are three problems with the drawings: 1) they are faked (p. 48), 2) Haeckel “stacked the deck by picking representatives that come closest to fitting his idea” (p. 49), and 3) he used the midpoint of development instead of the early stages as stated (p. 49). Haeckel made a claim known as ‘ontogeny recapitulates phylogeny’ or rather that we could see early embryos passing through their evolutionary history due to common ancestory, thus resulting in similarities at the beginning. This is no longer thought to be true, but the popular notion of ‘gill slits’ on embryos still lingers. Just to be clear: they are never functional structures for breathing. These ridges form various structures in the neck, the small bones of the ear, and other structures in the head and neck area.

Homology: Various homologies have been identified amongst organisms, but one of the most popular is the vertebrate limb comparison. Take home point: similarity does not indicate evolution on its own. For that we would need a mechanism of some sort. Tim Berra tried to propose a mechanism and inadvertently made an argument for the existence of an intelligent designer in what is now known as “Berra’s Blunder” (p. 52-53). He used similar Corvette models with small successive changes to show descent with modification. His mistake came in forgetting that a designer had to be present in the entire process. New mechanisms such as common developmental pathways and homologies due to similar genes have been proposed since and can be found in research journals.

Human fossils: First of all, the ape to man progression is just wrong even though it is still one of the most prominent images of evolution. The fossil record can easily be faked and misinterpreted. A further look on my part into molecular techniques of analyzing fossils is warranted along with some reading on radioisotope dating. All in all, these fossils, Java Man, Lucy, Neanderthal, etc. are usually considered with caution for due reason. Much more is needed to make conclusions on their origins and place in the history of the Earth.

So here’s my summary.

-Scientists are compelled by this evidence; therefore, it is worth learning so that we can bridge the gap and find an avenue for talking about God.

-These icons play a significant role in shaping some people’s lack of belief in God.

-We should act as missionaries to the scientific community. Remember this year at FBCM is about equipping the saints so that we can act locally or internationally to spread God's word.

Happy reading! Nicole

The secret things belong to the Lord our God, but the things revealed belong to us and to our children forever, that we may follow all the words of this law. –Deuteronomy 29:29

For now we see in a mirror dimly, but then face to face. Now I know in part; then I shall understand fully.

-1 Corinthians 13:12

Get wisdom, get understanding; do not forget my words or swerve from them. Do not forsake wisdom, and she will protect you; love her, and she will watch over you. Wisdom is supreme; therefore get wisdom. Though it cost all you have, get understanding.  -Proverbs 4:5-7