ATP Synthesis and Evolution

Evolution of G3PD Knowledge

The same technique used in chapter 13 could be used to calculate the knowledge in G3PD, but since this is a single protein the techniques discussed in chapters 4 and 5 will be used. The advantage of this approach is that it requires fewer assumptions.

   The knowledge will first be calculated assuming G3PD arose in the primordial soup. The analysis will then be repeated assuming that the protein evolved after the genetic code was in place. Because G3PD is a typical enzyme of about average size, there is every reason to believe that it is representative of most other enzymes.

   Fourteen amino acid sequences for G3PD were downloaded from this web site: http://us.expasy.org/sprot/. Seven are from higher animals or plants and 6 are from bacteria. Every effort was made to pick the sequences to maximize the diversity. The sequences were aligned using the computer program Clustal X. To obtain Clustal X visit: http://www-igbmc.u-strasbg.fr/BioInfo/. Once aligned the columns were scored by amino acid identity, and this file was saved as an output of the program. The file was imported into a spreadsheet, filtered, and manipulated. In the end, a spreadsheet was obtained that calculates knowledge. The techniques to do this manually are described in chapters 4 and 5. An automated system is necessary here because G3PD contains many more amino acids that insulin.

   Because large proteins tend to have only specific patches conserved (chapter 13), this analysis only uses the amino acids that are highly conserved to calculate knowledge. The alignment is shown on the next page.

Evolution of Molecular Knowledge in G3PD

Referring to the alignment on the previous page, notice that some columns have an * placed above them. In these columns, all of the amino acids are identical. All of these columns contribute to knowledge. The other columns must be manually inspected. Columns that only contain amino acids from the same group (see chapter 4) also contain knowledge. The 64 columns that meet these criteria show up as rows in table 14.1.

   To calculate the molecular knowledge using the genetic code, the amino acid group in each column is identified, and assigned a representative number of codons. For example, group 1 is composed of several amino acids that do not like water. This group includes alanine, methionine, leucine, isoleucine, and valine. Referring to table 4.1, alanine and valine each contributes 4 codons, methionine contributes 1, leucine contributes 6, and isoleucine contributes 3. Thus, the total number of codons that can code for a group 1 amino acid is 18. Thus, a group 1 column in the alignment (or the corresponding row in table 14.1) must contribute 3.32 x log ( 64/18) bits or 1.8 bits. The knowledge for the other groups is calculated in the same manner. For group definitions, see chapter 4, page 74.

Group Knowledge with Genetic Code
group 1 (leu, ile, val, ala, met) = 1.8 bits
group 2 (try, phe, trp)= 3.67 bits
group 3 (asp, glu)= 4 bits
group 4 (his, arg, lys)= 2.67 bits
group 5 (asn, gln)= 4 bits
group 6 (ser, thr)= 2.67 bits
group 7 (gly)= 4 bits
group 8 (pro)= 4 bits
group 9 (cys)= 5 bits


   The procedure outlined above is then repeated using the primordial soup not the genetic code to determine knowledge. That is table 5.1 sets the number of blocks for each group as explained in chapter 5. So from table 5.1, group 5 (asn and gln) contributes 400 + 400 = 800 blocks. But because there are 3,520,880 blocks in the truck (figure 5.1), the information is 3.32 x log ( 3,520,880/800) = 12.1 bits.

Group Knowledge with the Primordial Soup
group 1 (leu, ile, val, ala, met) = 3.1 bits
group 2 (try, phe, trp) = 11.5 bits
group 3 (asp, glu)= 7.4 bits
group 4 (his, arg, lys) = 14.8 bits
group 5 (asn, gln)= 12.1 bits
group 6 (ser, thr)= 10.2 bits
group 7 (gly)= 3.0 bits
group 8 (pro)= 12.2 bits
group 9 (cys)= 13.1 bits


   Given these results, molecular knowledge is easy to calculate. Simply identify each column in the alignment that contains only amino acids from one of the predefined groups. If the gene or protein is theorized to have evolved after life exists, assign bits to each column using the knowledge with the genetic code. If the gene or protein is theorized to have evolved before the genetic code, assign bits based on knowledge with the primordial soup.

   So referring to the alignment, column 11 is all G (which stands for glycine). So this column falls into group 7. It is assigned 3 bits with the primordial soup and 4 bits with the genetic code. Table 14.1 repeats this calculation for all positions that contain knowledge.


Table 14.1 GP3D Molecular Knowledge

   Only the last row of table 14.1 is important. It shows that GP3D contains 515 bits of knowledge with the primordial soup and 190 bits with the genetic code. The odds of this protein arising by chance are 1 in 1.4 x 10155 with the soup and 1.1 in 1057 with the genetic code. Also from the table, the average molecular knowledge per amino acid may be deduced. Since G3PD contains 330 amino acids, the average molecular knowledge per amino acid is 1.56 bits with the soup and 0.57 with the genetic code ( 515/330 and 190/330 respectively).                       

next: Primordial Soup Correction

home: Intelligent Design and the origin of life