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.

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