Tuesday, April 29, 2008

Fruit Fly 2


This is a picture of DNA stretched out (it normally looks like a twisted ladder). Don't worry if you can't understand the technical words. Just realize this is the way organisms carry genes--the features which are passed onto offspring. The DNA also is what is used to make the protein. It acts as a code. The bars in the middle come apart and they are "read" by another molecule, the RNA, to produce a mirror-image template. This template moves on to another part of the cell to eventually be read again. This time, the reading leads to new proteins.

The bars in the middle of the DNA are known as "base pairs." DNA has four different molecules that can be used as base pairs--two linked to each other along the rungs of the ladder. The reading is done by splitting DNA the long way and translating code of the four molecules in combinations of three that run along the length of the template. A new molecule of RNA is made and that is further processed to make protein. For example, a CGA will eventually be read as the amino acid "Arginine." That will be a part of the protein which is made by putting the amino acids together in correct order.The fruit fly has 180 million base pairs. After division and recombination through egg and sperm, they are passed along to individuals of the next generation which will once again have 180 million base pairs.

A description of the fruit fly from a website named "FlyBase" is in the links at right. The fruit fly has two life forms, the larva and the adult. There are also developments through embryo and pupa stages. The larva gets a shell around it as it metamorphosizes to the adult. The micro-processes by which it develops are being discovered. They are important and fit in with the discoveries of the genes and how they work.

It was previously thought that each gene translates into one protein in the organism. To remind you very briefly, sections of the DNA are divided into specific genes. The great surprise from the Human Genome Project is there are less genes than proteins. For example, there are only about 25-30 thousand genes in humans. There are around 100 thousand proteins, and these have further modifications done to them in the cell so that there are an estimated one million types of proteins in the human body.

The modifications to proteins in organisms come both before and after these proteins are made. There are differences between species, and I'll be talking about a variety of species, not just the fruit fly.

You have probably heard in the media that human and monkey DNA are very similar (varying reports of 95-99%). However, humans and monkeys are not 95% similar. A great deal of the differences are now being discovered in the regulatory levels of the genes. There are areas in DNA which had been called "junk DNA." These are between the genes and were thought to have little activity. Now they are thought to have regulatory affects on protein production.

As for the fruit fly, it is going to be an interesting study in how all these factors work together in an amazingly complex way.

Monday, April 28, 2008

Fruit Fly 1

The amazing complexity of the fruit fly can be seen from many angles. I've shown you the sequences of amino acids in just part of a muscle fiber in previous entries. I'd like to describe the way an individual fruit fly develops, which is going to take a few days. (I am also going to talk about other things in between). I'm hoping to find links that will show what I'm describing. Just click the link and then use the "back" key at the top left of your screen to get back to the blog. (I know most of you know this but I've been telling people about my blog that don't have a lot of experience in moving around the Internet.)

Let's begin easily by a general picture (not necessarily fruit fly) of a fertilized egg and how it starts to develop into specific organs. The picture is by the U.S. government, posted on Wikipedia, . Click here to see it and then the "back" key to return here when you're done looking at it. That was easy!

Sunday, April 27, 2008

Teach the Controversy

Though I was disappointed that Ben Stein's movie, Expelled , didn't have more science, I was glad that it exposes the divide of opinions about what science is and who can define it. Though the controversy in grade-school teaching of evolution is well-publicized, this dimension of university tensions over research is not. It was interesting that the Pope visited the US in the same week as Expelled opened. Pope Benedict asked his flock to live out our lives as Catholic believers. That we are entitled to view science as a study of God's creation is one area that needs a lot of work.

The disappointment in the lack of actual science in the movie is because the "Intelligent Design Science" is legitimate and amazing. Evolution is not just about bones anymore. It is about the genetics and molecular workings of life. That is what I am trying to convey in my blog, limited as I may be in my abilities to do so. More and more is being discovered each day, and it will take time to see the implications. But however grand Science may be, God is grander. I know not all believe that, but I do. Belief is different from reason, but not inferior.

The Intelligent Design movement is led by several organizations, including the Discovery Institute (link at right) which is featured in the movie Expelled. Many of the leading scientists in the movement are associated with Discovery. There are two aspects to their outlooks: scientific conclusions, and their personal faiths. Sometimes they come across as claiming that the Designer could be anyone or anything. That may be OK for non-Christians, but it is not OK for Christians. If a person says on a Sunday morning, "I believe in God the Father Almighty, creator of Heaven and Earth," and in the afternoon in an Intelligent Design conference says, "The designer could be anybody," there is a problem. Let's not quibble over the meanings of "design" and "creation." The point of the ID advocates is that science can go only so far. The reality of our inability to create an exact experiment of the events at the beginning of life will always keep us from knowing scientifically exactly what happened.

A problem still exists: the inevitable question comes to the teachers and scientists and writers explaining Intelligent Design Theory: Who is the Designer? Christians can't answer that question by saying, "I don't know."

The Discovery Institute advises to "teach the controversy." They say it is legal to present scientific arguments against evolution. A teacher may likely be confronted with a related question,"If evolution is wrong, what is right?" The teacher must be able to say, "I believe it is God who designed life." That should be the legal right of the teacher to have religious freedom in this country, but is that right given to him/her by the present laws?

Update 1/21/2013: My interest in Intelligent Design Theory (ID) has changed to what is called "Special Creationism," the belief that God created species separately and directly. Much of the biological science in ID is similar to Special Creationism.

Wednesday, April 23, 2008

Exponents



The way probability relates to biology and evolution can be controversial and yet is important. I'd like to talk about the simple mathematics of exponents for those who don't know much about it. Origin of life (OOL) and evolution are both important subjects in biology, and it helps to understand exponents in both cases.

The picture at the top shows 10 to the first, second and third powers. In my text, I use the ^ sign for the power after 10, such as 10^1, 10^2, 10^3. The exponent is the power to which the base, in this case ten, is multiplied by itself (e.g. 10^2=10x10). If the base is 10, the exponent, or power, can also stand for the number of zeroes after the 1. For instance, 10^1=10, 10^2=100 and 10^3=1000. You can see that the numbers increase dramatically as the exponents increase. If the line on your screen is about 3 1/2 inches as it is on mine, the next number, 10,000 would be at the end of a yard and the next, 10^5, at 30 feet.

The animation from Harvard about ATP Synthase (at right in Links) shows the cellular mechanism for construction of molecules which deliver energy to the rest of the cell (ATP). The mechanism would have had to be present in some of (all?) the earliest life on earth. The Synthase machinery has several components, each made of several sub-units. One of the proteins, ATP synthase subunit a, in the fruitfly has 224 amino acids in specific order. These are (from Uniprot, P00851):

10 20 30 40 50 60
MMTNLFSVFD PSAIFNLSLN WLSTFLGLLM IPSIYWLMPS RYNIFWNSIL LTLHKEFKTL

70 80 90 100 110 120
LGPSGHNGST FIFISLFSLI LFNNFMGLFP YIFTSTSHLT LTLSLALPLW LCFMLYGWIN

130 140 150 160 170 180
HTQHMFAHLV PQGTPAILMP FMVCIETISN IIRPGTLAVR LTANMIAGHL LLTLLGNTGP

190 200 210 220
SMSYLLVTFL LVAQIALLVL ESAVTMIQSY VFAVLSTLYS SEVN

Remember--the letters stand for amino acid abbreviations. For example, the A is for Alanine, D for Aspartic Acid, etc. (see Amino Acids--Wikipedia link at right).

The machinery would have had to be in working order from the days of the first bacteria. In fact, the bacteria E. Coli has more amino acids in this subunit than the fruitfly--271 (Uniprot, P0AB98). {By the way--scientists talk about viruses being simpler organisms which evolve, but viruses are not able to reproduce by themselves. They need other cells for the reproductive machinery in order to replicate and therefore could not have come earlier than those cells.} The bacteria, so far the simplest life forms which replicate, have over 1000 proteins in working order.

The probability atoms and molecules would have arranged themselves by chance into working machinery is astoundingly low. There are ways to figure the numbers, such as the probabilities of getting started with the strictly left "handedness" of amino acids as they are found in functional, living proteins (see Amino Acid Mirror Images link on right). Let's use the bacteria number of 271 amino acids for this sub-unit. For the ATP subunit shown above, just for the mirror-images to be only the L-(Levo for left) orientation by chance, we'd use 2 for the base because the outcome could either be left or right as it is in non-living nature. In cases of independent probability, you get the total probability by multiplying together each possible outcome. So that would be 1 in 2 for each amino acid to be L-oriented and 1 in 2^271 for the whole subunit to be L, which converts to about 1 in 10^81. The estimated number of particles in the universe is 10^80. Probabilities for the whole ATP Synthase molecule forming in the L-orientation by chance would be much smaller. William Demski defines what he calls the universal probability bound in his book, The Design Inference. He shows that all events in the universe, including chemical reactions, are within the number 10^150. That is a probability boundary for our universe. It's the multiplication of the number of particles in the universe, 10^80, times the maximum amount of events per second including chemical reactions, 10^45, times the number of seconds in an old universe of about 14 billion years, 10^25. If there is less than 1 chance in all the events of the universe for something to happen, we can be assured it didn't happen. (See The Design Inference, Cambridge UP, for a more precise definition of Universal Probability Bound.)

These numbers have caused some scientists to speculate on "Infinite Universe" theories. In that scenario, at least one of an infinite set of universes can by chance form life. Articles about infinite universes and life from the production of infinite universes have appeared in scientific journals. One interesting problem of the infinite universe (inflationary) theory that proponents have stated and now must consider: how can we know the probability of the formation of infinite universes?

Tuesday, April 22, 2008

Handedness (Chirality)


Twenty types of amino acids make up proteins. They come in mixed amounts of mirror images in nature. (It is called "chirality," pronounced ki-RAL-ity). This is a picture of one type of biological amino acid, alanine. The amino acids are made of atoms (carbon, oxygen, nitrogen, hydrogen). In biological life, only one of these "hands," the left one, is found. This is one of the first puzzles of origin of life. John Lennox (in his book, God's Undertaker) discusses the probability of just one protein of one hundred amino acids (an average number for proteins) forming by chance in the way it has. It would be 1 in 2^100, or 1 in 10^30 (a 1 with 30 zeroes after it). The number of seconds in universe so far (if it is about 13-14 billion years old) is less than 10^18, which gives you an idea of size of the numbers. The base 2 stands for the left or right hand of the amino acid that could be included in that protein by chance.

This number does not factor in that there are hundreds of types of amino acids found in nature, but only 20 types in biological life. It also does not start to evaluate whether the amino acids make a protein which can be used in nature. Living proteins have shapes which give them their ability to act, just like toasters and coffee machines have different shapes for different jobs.

Saturday, April 19, 2008

Expelled Movie

My husband, our friend George and I saw the movie "Expelled" yesterday. It's going to cause a lot of flak, I think, and it's good people will be made aware of the bias against believers in the world of academic science. However, I wish the movie had more about science itself. That prompted me to get the link to an animation from Harvard about cell biology. It is a video of what is called ATP Synthase, which makes the energy-carrying ATP molecule. It works in a membrane inside the cells--and each human has an estimated 75 trillion cells! You should be able to find the link in the right column.

Thursday, April 10, 2008

Woman at Well

The woman at the well is one of my favorite Bible Stories. It's in the Gospel of John, Chapter 4. I've added a link to it--select "Well Woman" at right to take you to the NIV version in Gospelcom.net.