Monday, March 31, 2008

Who is Designer?

Who is the designer in Intelligent Design Theory? Many of the advocates say the designer could be anything or anybody. I won't get into what their motivations are or what other people speculate the motivations are. Though many say theology is not involved, I believe it is.

I think Intelligent Design Theory can be understood and appreciated by someone who does not believe in God. But they still may feel they don't know who God is. However, if a person is a Christian, that person knows who the designer is. There are creeds in most Christian churches that begin:

Nicene Creed
We believe in one God, the Father, the Almighty,
maker of heaven and earth,
of all that is seen and unseen.

Apostles’ Creed
We believe in God, the Father almighty,
creator of heaven and earth.
We believe in Jesus Christ,
his only Son, our Lord.

For the Christian, the Designer is the God of the Bible, the God of One Essence with Three Persons (Father, Jesus Christ the Son, and Holy Spririt). The first chapter of the Bible tells us that God created plants, animals and persons.

I've seen that some people think the label "Designer" is a step down for God from "Creator." They say all He has to do is think and something is Created. Well, His thoughts are way above our thoughts and I don't know how He thinks or creates. But at this point I'd like to think He has had some choices and decided which was the best. He has made persons able to walk, talk, and make our own creations. He has given humans brains to think about important things like religion and science.

Sunday, March 30, 2008

Muscle, Probability

This is another protein from the fruitfly. This protein is needed just to get the DNA started in a cell so that the cell becomes a muscle cell. It is entry P22816 at UniProt where you can find the sequence, the people who did the work to find the sequence, and other infomation about it, like what it does. Remember, the letters stand for amino acids which can be seen in the Wikipedia link to amino acids at right.

10 20 30 40 50 60
MTKYNSGSSE MPAAQTIKQE YHNGYGQPTH PGYGFSAYSQ QNPIAHPGQN PHQTLQNFFS

70 80 90 100 110 120
RFNAVGDASA GNGGAASISA NGSGSSCNYS HANHHPAELD KPLGMNMTPS PIYTTDYDDE

130 140 150 160 170 180
NSSLSSEEHV LAPLVCSSAQ SSRPCLTWAC KACKKKSVTV DRRKAATMRE RRRLRKVNEA

190 200 210 220 230 240
FEILKRRTSS NPNQRLPKVE ILRNAIEYIE SLEDLLQESS TTRDGDNLAP SLSGKSCQSD

250 260 270 280 290 300
YLSSYAGAYL EDKLSFYNKH MEKYGQFTDF DGNANGSSLD CLNLIVQSIN KSTTSPIQNK

310 320 330
ATPSASDTQS PPSSGATAPT SLHVNFKRKC ST


Before you can have a muscle, you need the cells of the embryo to differentiate and each become one of the hundreds of specialized cells of the body. The embryo starts to form in a certain pattern, then some parts of the embyro outside the cell give signals that get to the inside of the cell so that the cell then starts with producing proteins called transcription factors that bind to DNA. The DNA will then produce other proteins, like one of the muscle proteins that is in another entry in my blog (March 27). The cell therefore becomes a muscle cell with muscle fibers inside that contract when the muscle is moved. Of course, you need other proteins called enzymes to help get the process working, like the ones that copy the DNA, called RNA polymerases. That would be this one:

10 20 30 40 50 60
MPKEQFRASA LNKKISHVQF GISGADEIQQ EALVRIISKN LYQAQRQPVP YGVLDRRMGI

70 80 90 100 110 120
STKDAMCETC GQGLNECIGH FGYLDLALPV FHIGHFRSTI NILQMICKVC AHVMLKPEDR

130 140 150 160 170 180
QLYEKKLHNP NFSYLGKKAL HVQMLAKAKK VTKCPHCGSP NGGVKKGPGL LKILHDPYKG

190 200 210 220 230 240
RKMDSLFTSN MNEMLRSTQT NRDLNSTLGN YSTAEELTPL MVLDLFEQIP QRDVALLGMC

250 260 270 280 290 300
SHDAHPKHLI VTRVFVPPAC IRPSVLSEVK AGTTEDDLTM KQSEILLIND VIQRHMATGG

310 320 330 340 350 360
KIELIHEDWD FLQLHVALYF HSEISGIPIN MAPKKTTRGI VQRLKGKQGR FRCNLSGKRV

370 380 390 400 410 420
DFSGRTVISP DPNLMINQVG VPVRVAKILT YPERVNPANI RHMRELVRNG PSMHPGANYV

430 440 450 460 470 480
QQRGSSFKKY LAYGNREKVA QELKCGDVVE RHLRDGDIVL FNRQPSLHKM SIMCHRAKVQ

490 500 510 520 530 540
PQRTFRFNEC ACTPYNADFD GDEMNLHLPQ TEEARAEALI LMGNQSNLVT PKNGEILIAA

550 560 570 580 590 600
TQDFITGGYL LTQKEVFLTK EEAMQLAACF LANEDSTMHI KLPPPALLKP RRLWTGKQMF

610 620 630 640 650 660
SLLMRPNDDS QVRLNMVNKG RNYTRNKDLC SNDSWIHIRN SELMCGVMDK ATMGSGTKQC

670 680 690 700 710 720
IFYLLLRDFG ESHATKAMWR LARNRGFSFG ISDVTPSKKL LQHKELLLNN GYAKCNEYIE

730 740 750 760 770 780
LLKAGTLQCQ PGCTPEETLE SVMLRELSAI REQAAKTCFA ELHPTNSALI MALSGSKGSN

790 800 810 820 830 840
INISQMIACV GQQAISGKRV PNGFENRALP HFERHSAIPA ARGFVQNSFY SGLTPTEFFF

850 860 870 880 890 900
HTMAGREGLV DTAVKTAETG YLQRRLVKCL EDLVVHYDGT VRNAVNEMVD TIYGGDGLDP

910 920 930 940 950 960
VSMETRNKPV DLVHQYDNLR AQHPQGKDRP LNAEEMSEAL ETLLRTPEFA EARDDFKLDV

970 980 990 1000 1010 1020
RNHINTVSKR IGQLQKRYEK CIDLCHQIEC LTTEQLLQFV RRINDRYNRA VTEPGTAVGA

1030 1040 1050 1060 1070 1080
IAAQSIGEPG TQMTLKTFHF AGVASMNITQ GVPRIVEIIN ATKTISTPII TAELENCHSM

1090 1100 1110 1120 1130 1140
EFARQVKARI EKTTLAELSS YVEVVCGPYS CYLAIGVDMA RIKLLGLHID LDTIVFSILK

1150 1160 1170 1180 1190 1200
SRMRVKPTQV EVVASQSRIV VRVEATRTST INAELARLAL SLQNVVVAGL PNINRAVIAV

1210 1220 1230 1240 1250 1260
DDARQPPTYK LCIEGYGLRD VIATYGVVGK RTRSNNICEI YQTLGIEAAR TIIMSEITEV

1270 1280 1290 1300 1310 1320
MEGHGMSVDW RHIMLLASQM TARGEVLGIT RHGLAKMRES VFNLASFEKT ADHLFDAAYY

1330 1340 1350 1360 1370
GQTDAINGVS ERIILGMPAC IGTGIFKLLQ QHEDKQVPPI EPTICSSLNL LPSKTT


At least at the website it is inferred from studies that this is RNA polymerase. The entry is A8JUY3 at UniProt.

Let's talk about probability that life could have happened by chance. A well-known metaphor for chance is the image of one million monkeys sitting at a million typewriters. If given enough time, some say, they will type out by chance the works of Shakespeare. However, the mathematics of probability shows that even for the old-earthers, the 14 billion years of the universe so far has not been nearly enough time for this to happen. For one million monkeys on keyboards with all the letters, a space and period keys (a total of 28 units) typing continuously at 60 words per minute, it would take seconds to type any 31-unit string. But to cover all possibilities except duplications (or on-average), they would need about 7 thousand trillion trillion trillion years to write the specific 31-unit string: It was a dark and stormy night.

A really good book about probability of life is by John Lennox, a teacher of mathematics at Oxford University. It's published by Lion and called God's Undertaker: Has Science Buried God? He shows the vast improbability both of random beginnings of life and evolution.

Some say that possibly billions of planets exist in the universe and so life was inevitable. William Dembski has showed that the maximum possible events, including chemical reactions, in the universe is about 10 to the 150th (I'm going to use ^ for the exponent from now on--10^150 in this case). Billions of planets (10^9 or so), are not enough for a random start to life.

The simplest bacteria I've seen so far has 1100 proteins. Cyanobacteria, which can make all their own energy and reproduce, unlike virus or mitochondria, have about 3.5 million DNA base pairs. E. coli bacteria have over 4000 proteins. The odds for these structures starting by chance are far less than 1 in 10^150.

Even evolution, where you supposedly have a start in DNA and proteins which can change by mutation over generations, cannot overcome the numbers when it comes to combinations needed for regulatory signals and feedback mechanisms.

Saturday, March 29, 2008

NCBI

The link at right for the National Center for Biotechnology Information has things like gene sequences, online text books about biology, and other good stuff.

Thursday, March 27, 2008

Muscle Protein

Now that I put links to show you what proteins and amino acids and DNA look like, I'd like to start putting into my blog some of the amazing discoveries in biology of the last few years. First, we'll start with the fruit fly. That's a critter that has been researched extensively. It has muscle proteins, just as many animals do, including humans. It uses muscles to move in various ways. See the set of muscles here. The muscles are made of different components which are pictured here. One part of the muscle fiber, myosin, is made of 3 sets of proteins: 2 heavy chains of myosin and 4 light ones. Below is the amino acid sequence for the heavy chain. I got this from the UniProt website (I have a link to their home page). I also have a link to muscle in Wikipedia if you want more information on muscle. Click the pictures to see bigger versions.

The letters each stand for an amino acid. For example, M is for methionine and P stands for proline. The numbers tell you how many there are (they are more spread out on UniProt). You can look this one up from the UniProt site by going to the QUERY BOX at the top of the page and putting in the code for this one which happens to be P05661 (the 0 is a zero) or just click here. The file you get shows you the protein sequence, the people who did the work on it, and some information about it. It's fascinating.

10 20 30 40 50 60
MPKPVANQED EDPTPYLFVS LEQRRIDQSK PYDSKKSCWI PDEKEGYLLG EIKATKGDIV

70 80 90 100 110 120
SVGLQGGEVR DIKSEKVEKV NPPKFEKIED MADMTVLNTP CVLHNLRQRY YAKLIYTYSG

130 140 150 160 170 180
LFCVAINPYK RYPVYTNRCA KMYRGKRRNE VPPHIFAISD GAYVDMLTNH VNQSMLITGE

190 200 210 220 230 240
SGAGKTENTK KVIAYFATVG ASKKTDEAAK SKGSLEDQVV QTNPVLEAFG NAKTVRNDNS

250 260 270 280 290 300
SRFGKFIRIH FGPTGKLAGA DIETYLLEKA RVISQQSLER SYHIFYQIMS GSVPGVKDIC

310 320 330 340 350 360
LLTDNIYDYH IVSQGKVTVA SIDDAEEFSL TDQAFDILGF TKQEKEDVYR ITAAVMHMGG

370 380 390 400 410 420
MKFKQRGREE QAEQDGEEEG GRVSKLFGCD TAELYKNLLK PRIKVGNEFV TQGRNVQQVT

430 440 450 460 470 480
NSIGALCKGV FDRLFKWLVK KCNETLDTQQ KRQHFIGVLD IAGFEIFEYN GFEQLCINFT

490 500 510 520 530 540
NEKLQQFFNH IMFVMEQEEY KKEGINWDFI DFGMDLLACI DLIEKPMGIL SILEEESMFP

550 560 570 580 590 600
KATDQTFSEK LTNTHLGKSA PFQKPKPPKP GQQAAHFAIA HYAGCVSYNI TGWLEKNKDP

610 620 630 640 650 660
LNDTVVDQFK KSQNKLLIEI FADHAGQSGG GEQAKGGRGK KGGGFATVSS AYKEQLNSLM

670 680 690 700 710 720
TTLRSTQPHF VRCIIPNEMK QPGVVDAHLV MHQLTCNGVL EGIRICRKGF PNRMMYPDFK

730 740 750 760 770 780
MRYQILNPRG IKDLDCPKKA SKVLIESTEL NEDLYRLGHT KVFFRAGVLG QMEEFRDERL

790 800 810 820 830 840
GKIMSWMQAW ARGYLSRKGF KKLQEQRVAL KVVQRNLRKY LQLRTWPWYK LWQKVKPLLN

850 860 870 880 890 900
VSRIEDEIAR LEEKAKKAEE LHAAEVKVRK ELEALNAKLL AEKTALLDSL SGEKGALQDY

910 920 930 940 950 960
QERNAKLTAQ KNDLENQLRD IQERLTQEED ARNQLFQQKK KADQEISGLK KDIEDLELNV

970 980 990 1000 1010 1020
QKAEQDKATK DHQIRNLNDE IAHQDELINK LNKEKKMQGE TNQKTGEELQ AAEDKINHLN

1030 1040 1050 1060 1070 1080
KVKAKLEQTL DELEDSLERE KKVRGDVEKS KRKVEGDLKL TQEAVADLER NKKELEQTIQ

1090 1100 1110 1120 1130 1140
RKDKELSSIT AKLEDEQVVV LKHQRQIKEL QARIEELEEE VEAERQARAK AEKQRADLAR

1150 1160 1170 1180 1190 1200
ELEELGERLE EAGGATSAQI ELNKKREAEL SKLRRDLEEA NIQHESTLAN LRKKHNDAVA

1210 1220 1230 1240 1250 1260
EMAEQVDQLN KLKAKAEHDR QTCHNELNQT RTACDQLGRD KAAQEKIAKQ LQHTLNEVQS

1270 1280 1290 1300 1310 1320
KLDETNRTLN DFDASKKKLS IENSDLLRQL EEAESQVSQL SKIKISLTTQ LEDTKRLADE

1330 1340 1350 1360 1370 1380
ESRERATLLG KFRNLEHDLD NLREQVEEEA EGKADLQRQL SKANAEAQVW RSKYESDGVA

1390 1400 1410 1420 1430 1440
RSEELEEAKR KLQARLAEAE ETIESLNQKC IGLEKTKQRL STEVEDLQLE VDRANAIANA

1450 1460 1470 1480 1490 1500
AEKKQKAFDK IIGEWKLKVD DLAAELDASQ KECRNYSTEL FRLKGAYEEG QEQLEAVRRE

1510 1520 1530 1540 1550 1560
NKNLADEVKD LLDQIGEGGR NIHEIEKARK RLEAEKDELQ AALEEAEAAL EQEENKVLRA

1570 1580 1590 1600 1610 1620
QLELSQVRQE IDRRIQEKEE EFENTRKNHQ RALDSMQASL EAEAKGKAEA LRMKKKLEAD

1630 1640 1650 1660 1670 1680
INELEIALDH ANKANAEAQK NIKRYQQQLK DIQTALEEEQ RARDDAREQL GISERRANAL

1690 1700 1710 1720 1730 1740
QNELEESRTL LEQADRGRRQ AEQELADAHE QLNEVSAQNA SISAAKRKLE SELQTLHSDL

1750 1760 1770 1780 1790 1800
DELLNEAKNS EEKAKKAMVD AARLADELRA EQDHAQTQEK LRKALEQQIK ELQVRLDEAE

1810 1820 1830 1840 1850 1860
ANALKGGKKA IQKLEQRVRE LENELDGEQR RHADAQKNLR KSERRVKELS FQSEEDRKNH

1870 1880 1890 1900 1910 1920
ERMQDLVDKL QQKIKTYKRQ IEEAEEIAAL NLAKFRKAQQ ELEEAEERAD LAEQAISKFR

1930 1940 1950 1960
AKGRAGSVGR GASPAPRATS VRPQFDGLAF PPRFDLAPEN EF

You may wonder why I put the sequences of part of a muscle fiber of a fruitfly on my blog. I want to show you the type of information that is used in Intelligent Design Theory. This fiber has over 1900 amino acids in a row (called a sequence). There are 20 kinds of amino acids in an order that works only for this muscle fiber. That is called a specified order. It is also called complex because of all of the amino acids needed. In Intelligent Design Theory (ID), the biology of living systems is believed to be Irreducibly Complex. In other words, you can't get the muscle of the fruitfly to work if it doesn't have all or at least most of these amino acids. IDT also says that biological machines such as muscle are of Specified Complexity. The amino acids have to be specifically where they are to work. These two components of ID have been written about by Michael Behe in Darwin's Black Box (Simon and Schuster, 1996) and William Dembski in Intelligent Design (InterVarsity Press, 1999).

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, March 26, 2008

DNA, RNA and Genes


DNA and RNA make amino acids into protein (click here for picture in Wikipedia). The letters in the Wikipedia picture stand for subunits of DNA, RNA and proteins, which I will get to later. DNA is divided into genes and has other areas that don't make genes directly. An overview of the cell making proteins from DNA is in the link at right (Cell).

The Human Genome Project found that humans have about 20-30 thousand genes. This was a surprise, since many thought there would be at least 100,000. The genes are used as a code to make protein. However, there are about 1 million variations of proteins. Therefore, the genes must be regulated so that they can make more than one kind of protein per gene. Now scientists are discovering that proteins themselves and RNA, which copies the DNA, are involved in regulating types and amounts of protein. We will get into details later.

Tuesday, March 25, 2008

Easter

I hope you all enjoyed a blessed Easter. My husband and I went to mass and then family for dinner. I thought about all the worshippers of Christ through the world and felt a part of it all. TV news brings pictures of services all over the world and it is so special to feel part of that. Christians are truly brothers and sisters, joined in a wondrous way.

If you are interested in learning more about amino acids and proteins, you can always go to Wikipedia. I will put a few links there, because they do have very good pictures and descriptions and references to papers, books, etc. I think it is a good place to start to learn something. I will put a few links so you can see what I mean if you are not familiar with it.

Friday, March 21, 2008

Amino Acids, Proteins


Some of the links on the right connect to pictures of proteins, genes and amino acids. Don't be afraid of the terms--just read what you can and look at the pictures. This blog is here to help you learn the wondrous workings of biology. I will also make links right in the entries so you can use those as you go. You can also click on the pictures in the entries, such as this one of amino acids, to get a better look. I got this list from a Google search, but the page is no longer there.

The amino acids pictured here make up the proteins, which are a large part of our body (the link to proteins shows one example--myoglobin). The proteins need to be in just the right shapes and sizes to do their various jobs . Though there are hundreds of amino acids, only 20 are used in varying sequences to make up the proteins. They are in specific sequence, just like the letters of this sentence are in specific sequence to give it meaning. When I give you a list with the amino acids that make up the proteins, the letter has the abbreviation for one of the amino acids (for example in this post). Each one would have to be substituted into the list to show the whole protein. There are other cell machines which make the amino acids into proteins. We will talk about them in entries to come.
There may be as many as 1 million variations of proteins in the human body. It is amazing to imagine the specific order of 20 amino acids can do so much!

Saturday, March 15, 2008

Introduction

I am a Catholic and believe in One God, the Father, Son and Holy Ghost, 3 persons of one essence.

I have an education which includes both biology and theology. My husband is an aeronautical engineer. We are interested in the arguments concerning Intelligent Design.

God is complicated and so is science. It is important we try to learn as much as we can to make valid arguments. We must be willing to hear from all sides.

Saturday, March 8, 2008

Psalm 117

1. O Praise the Lord, all ye nations:
Praise him, all ye people.
2. For his merciful kindness is great toward us:
and the truth of the Lord endureth forever.

Praise ye the Lord.

(KJV)